Yeah, if it was a probe issue you usually would be bounced off from the LM and not go through it. I guess you will have to post your scenario, best just before docking, so I can check what is going wrong.
Ok. Also after the SLA panels eject I found that the CSM is a little off when compared to the LM, it's not directly above it. I attached a screenshot I hope you can see it. I waited for a while to let the particles from staging disappear (I never did get that fixed).
You can find instructions for the MFD under \doc\Orbiter.pdf section 15.5. Basically, you need to make sure the X and the + are centered, and the arrow on the outer ring is at the 12 o'clock position.
The X indicates error in pitch and yaw.
The + indicates error in Y and Z.
The arrow at the outer ring indicates error in roll.
The yellow arrow extending from the center shows the X and Y error trend.
(This is only valid for a CSM active docking. A LM active docking has 120 degrees offset)
Since docking is handled by Orbiter, if you're not aligned according to the MFD, even if the docking target is aligned in the COAS, you won't dock and instead pass through the LM.
Rotate to put the nose on the ISS, then set up for docking as follows.
If you are only a kilometre or so from the ISS with zero RVel, the Sync MFD has done its job and you can power it down to give better visibility for docking (assuming you are using the no-panel view). But if you have Orbiter Sound installed, you may be hearing an annoying beep now – the radar proximity warning. You can turn it off before closing the left MFD.
On the left MFD, click [SEL], [Radio/MP3 panel], [RAD], and [PWR] (off).
On the right MFD, click [SEL], [Docking], [NAV] (three times), then [HUD].
This will set up the docking MFD to use NAV4 which has been set to 137.40 MHz, the IDS (instrument docking system) frequency for ISS docking port D-01. The ISS in Orbiter has five docking ports – you can find this and other detailed information in the CTRL-I (info) dialog box. Why port D-01? It worked out OK in the recording, although it was not pointing in my approach direction. Feel free to try out other ports and see if they seem easier to approach (you can cycle through the four defined frequencies with [NAV] and send the port info to the HUD with the [HUD] button).
Use lateral LIN (left/right, up/down) thrusters to move the –V[ISS] symbol onto the outer docking boxes as shown below.
The docking boxes are like a “road in the sky” leading to the selected docking port. If you just head directly for the ISS, it will be hard to get lined up with the docking port. The docking boxes are like an ILS glide path for a runway (if you are familiar with instrument approaches).
Use forward RCS thrust to start closing on the boxes.
Here’s where you need some patience (or some 10x warp) since 740 m at 1.5 m/s will take 8 minutes to cover. This is nothing in real world docking (the Space Shuttle takes days to rendezvous with the ISS, hours for the final few hundred meters and docking), but you can get tired of waiting. You can stay fairly slow and use 10x time acceleration, or you can try some small bursts of main and retro engines (better open the retro doors to be ready, Control-Space).
When you get near one of the outer docking boxes, switch to rotation and turn and face the ISS.
Recall that KEYPAD-/ toggles between LIN and ROT (or you can use the screen buttons in the upper left corner of the no-panel view). You may not really be “inside” a box at first – you may be above or below or otherwise offset from it. You will probably need more literal translation as well as rotation to get into position to “slide down” the docking boxes, and you may pass the ISS at some point and see your closing velocity (CVEL) go from positive to negative – this is OK since you are going to one of the outer docking boxes to get lined up before trying to close the range for docking (you could also get lucky sometimes and pick a docking port whose IDS boxes point right toward you, saving you a lot of manoeuvring). Don’t worry about perfect alignment or position now – just pointing at the ISS with the docking boxes somewhere in front of you is OK for starters (as in the example below).
This manoeuvring can be confusing at first. Feel free to use the outside view to get a better feel for the 3D geometry of your approach. You won’t see the docking boxes, but by spinning your view with the right mouse button, you may be able to better visualize the situation.
If your closing velocity (CVEL) is positive, use forward or backward LIN thrust (KEYPAD-6/9) to drive it close to zero.
CVEL of around 0.02 or 0.04 is OK – you just don’t want to close the range much more until you can really get the IDS boxes in front of you and start to get aligned rotationally (this is the X symbol shown in red in the Docking MFD above), and somewhat aligned laterally (that’s the green plus sign). Just having the X and the + appear on the MFD is good enough for now.
Use lateral (left/right/up/down) LIN thrusting to put the –V[ISS] HUD symbol inside one of the outer boxes and thrust toward it.
Remember that this symbol shows where you are heading relative to the ISS. It’s OK to have a positive CVEL if it’s taking you into one of the boxes (the picture is intentionally cropped to show mainly the boxes, showing only part of the ISS itself).
B]When you get nearly inside one of the boxes, switch to ROT and use pitch, yaw, and roll to point at the ISS and get lined up with the boxes (double-line at the top).[/B]
Once you get in the “right” orientation things will seem a lot less confusing and you can begin to mentally separate your problems as rotational (pointing, shown by the MFD X) and lateral alignment (shown by the MFD + sign). Rotation should be solved first, even if you feel you are too high or too low as a result. Closing a bit fast in this view (1.18 m/s), need to slow down.
Use linear RCS thrusters to slow CVEL to nearly zero again.
You need to stabilize several hundred meters away to complete your alignment with the HUD boxes and get ready to fine-tune the alignment with the Docking MFD.
Use rotational RCS thrusters to get the Docking MFD X symbol lined up with the centre of the rings (angular alignment).
Rotate toward the X – if it’s above the centre in the MFD, pitch the nose up (KEYPAD-2) if it’s to the left, yaw left (use Kill Rotation as needed). It can be a little off now but get it mostly lined up (the X will turn white). This will make your nose-tail axis parallel with a line sticking straight out of the docking port. With this solved, you will know that any deviation you see is due to lateral shifts and not due to looking from a skewed direction.
With angular alignment solved, use linear thrusters to line up the MFD “plus sign” with the centre of the rings for lateral alignment. Thrust toward the MFD cross to move it – think of this as the target, and if the target is to the left, you thrust to the left. You will also notice an arrow that appears on the MFD to show the direction and magnitude of your lateral motion. This will usually take a number of tries and constant adjustment until you get a feel for it. You may also find that the angular alignment drifts a little – if so, switch to ROT and correct it, using fine thrusters (CTRL-KEYPAD) if necessary to really center it (it should stay centered pretty well on its own unless you have gravity gradient torque and/or nonspherical gravity sources checked in the Launchpad Parameters page – these settings are more realistic but can make docking a bit more challenging). Don’t forget to switch back to translation (LIN) RCS mode.
When angular and lateral alignment is both good and relatively stable, use LIN forward thrust (KEYPAD-6, not main engines) to start to close on the port.
You can close at 0.3-0.5 m/s or so, slow enough to make corrections but fast enough to see progress. When you get within 5 m or so, you should slow to about 0.10 m/s for final docking. When you are stable, you will find that the -V[ISS] cross will sit just a bit higher than the docking port (because the DG’s docking port in the nose is lower than your eye point). The key point is “when you are stable” because if there is any lateral velocity, the cross will drift. Use both the outside view and the Docking MFD to keep track of what’s happening and try to keep everything “happy.” Unless the MFD X gets off-centre, use only LIN thrusters from now on – no rotations.
Slow to around CVEL 0.1 m/s to close and dock.
If you get substantially out of alignment when within DST 75 m or closer, it’s best to back up to 100 m or so, reduce separation rate to near zero, and fix your line-up, then start to move in again. It’s quite hard to fix a bad alignment when you are very close – as with a good landing in an aeroplane, the secret of good docking is a good approach. Congratulations on docking!
Credits: @FlyingSinger and @AndyMc. I've used the same method but with "DG-ISS" playback.