This is probably due to non-sherical gravity sources. Phobos is a tough target by any means. In the scenario included with the DGIV you start with your orbit matched to Phobos', and getting to that point is tricky. As you've noticed, Phobos has very little gravity, and won't capture your craft if you have more than a very slight R-Vel. Landing on Phobos is more like a docking manuever than a nomal capture/landing. First you'll have to match orbits. Sounds like you can get the planes aligned, and a sync within a few kilometers is fine. Use intersect mode when syncing. If approaching from a lower altitude, try to be the last to arrive at the intersect. If coming in from a higher orbit try to be first. Now for the next step - eliminating the relative velocity.
If you are using one of the scenarios with a Prelude base in Phobos (recommended) you can use VTOLMFD to help you eliminate R-Vel. Otherwise SurfaceMFD (reference Phobos) can be used. As you approach Phobos ensure you HUD is in Orbit mode, referenced to Mars. Point the nose at the center of Phobos. If you are coming in from lower orbit you will be travelling slower than Phobos and should be "behind" Phobos. Roll so that the Prograde Velocity marker is below the nose reticle (directly below center of screen, off screen OK). Watch your verticle speed (VS ) and vertical acceleration (VACC) on SurfaceMFD (ensure it is referenced to Phobos) You should have a negative VS. When VS is approaching zero (when we are closest to Phobos) use the main thrusters to maintain zero VACC, as close to zero VS. Up to 100 m/s VS is OK. At the same time, use the hover engines to move the Prograde Velocity marker unil its near, or on, Phobos. Maintain a small (100 m/s or less) negative VS until you are close to Phobs. Use translational RCS to keep the Prograde Velocity marker pointed in the direction you want to go and find the Prelude Base. Using small bursts of RCS, manuever yourself to the pad and land. Remember to keep the vertical speed and ground speed shown by SurfaceMFD small, less than 100 m/s total. patience is essential, use short bursts of 10x time accell rather than increase velocity.
If you are coming in from above Phobos you will be traveling faster than Phobos and should have timed your arrival to be in front of Phobos. Use the same procedure as above EXCEPT: Once pointed at Phobos, roll so that the RETROGRADE indicator is ABOVE the center of the screen, and use the retrograde indicator to target your "heading" around Phobos.