I've been seeing the same thing for a little while now. Planes involved in naval combat often can't move during the non-combat phase, and must crash. I'm running svn 2832, and the last couple games were WW2v3 1942.
This bug is still currently active. There are actually 3 scenarios:
1) attack an undefended transport (only trans)
2) attack a submarine (only subs)
3) attack a sub and trans (only subs and trans)
You only fixed case 1. If I fire up a game and attack cases 2 and 3, I
can move my sea units after the battle is over.
I tried looking in the code for the sections that delt with those cases,
but i could not find anything, so I'm leaving this one to you.
ps, I also fixed case 1, so that it only sets the attacker's Sea Units'
movement to Zero (aircraft should not be set to zero).