I too have encountered this problem with both Germany, SU and USA force pools. I have been able to reproduce it almost at will from both saved games and from the start of new ones.
This is what happens (assume now other units in the province):
Load a para unit onto a aircraft transport. Now the military screen is clear. Click on the transport. On the military screen you will see only the para unit although the transport is highlighted on the map. If, however, you click very carefully on the bottom left corner of the highlighted unit, you may be able to pull up the transport on the military screen. Once this is accomplished you can continue by right clicking the province you wish to para drop or rebase to. If you forget yourself and have the para on the military screen and right click elsewhere, the game will CTD.
There is a work around. If you have multiple para units in a province, do not merge them. Same goes for the transports. Leave them separate and then load them individually. Transporting to different areas will then work. Just be sure that the plane shows on the military screen each time and not the loaded para.
Another work around it to ensure that there is at least one other unit (of any type) in the province. I have ended up with a Tac, para, transport combo to move around and conduct para drops. There is no need for the Tac to accompany the transport on the para drop mission.
It seems to me that there may be a problem with the stacking/ loading code. Maybe the game sees the transport as being loaded onto the para instead of visa versa. Just a thought.
I have been playing the game for three weeks now and greatly enjoy it. It fills my WIF need as no one in this small town plays the board game. Thanks for the great game and supporting it post release.
PS: Sorry, I purged my saved games but could make more if ya wish.