If you open my scenario and you see that the "Orbit eject" program is displaying something, then the two MFDs ARE correctly syncronized.
Otherwise, the "Orbit eject" program would give you an error (no graph, only a yellow text), since you've selected "Course" but it can't read the course because it's not linked to the other MFD.
I don't know why you think they are not linked, they actually are.
Are you using version 5.5?
Just so you make sure my scenario is working, left MFD should be Target intercept, right one should be Orbit eject program.
EDIT
Another thing. I asked for clarifications in the italian orbiter forum and this is what I got:
- EIn (plane alignment error) must be set as close to zero as possible, changing TIn;
- the IMFD always makes you reach the center of the target planet, so you will always encounter the planet;
- but of course you will need MCCs at some point.
So if you miss Venus:
-bad MCCs;
-bad EIn *;
-or that problem about sharing one MFD with the other.
Other things, like choosing an ejection/intersect time or another, just change the required dV, so that's not a cause of failing the encounter.
* I totally forgot the EIn variable. :facepalm: Here's about it from the manual:
EIn: Escape/Ejection Inclination.
An angle between escape vector and the orbital plane of the ship. In a transfer program, it is also the angle between the orbital plane of the ship and the target position at the time of interception.