I am delighted to read Your story. After two weeks of being almost cutten off the net - such dose of heavy action was a balm on my soul bored in the office after two weeks of vacation.
The cause of noncompatibility is P R O A B L Y (!!!) simple.
I have called it: "multiresolutioning".
See this:
1. Japanese player cannot afford loosing any of his major ships like big flattops and battleships.
2. Major naval clashes are causing looses (sometimes

3. Japanese player can do as many resolution phases as he wants, [I have proposed recomposition of turn and execution phases (EP) in order to have allied player resolving the EP in secrecy (unable to see the results) then the VCR should be available for Japanese side to do the turn, but noone important was iterested ?]
4. After first mulitresolution - the price is noncompatibility. Japanse player sees always the right video (VCR) and the right battle reports (BR), but the program seems to use some differently randomized values while showing the VCR to Allied player, giving him even false BR sometimes (battles that Your Japanese opponents have to describe to You because You don't see them anywhere). Never had enough patience to count it and make further studies.
5. After first "multiresoluting" there is no known to me way to restore things like they were before.
(I haven't tried to back up one turn and put the savefiles in "freshly" downloaded game directory, eventually cleaning up the system registry.)
If theory described above is correct (it explains also why the bug is showing after major battles) there's no way to make it solved forever until the VCR is done by Japanese side or done and visible by allies [WIR is having 100 times better bug, but that's a topic for another story

Second explanation may be that the game itself goes corrupted after certain amount of turns under PBEM game. Mikka should be able to check it out I believe. As stated before - I'm not patient enough even to try a game against myself.
Maybe somebody got other idea ?
Who cares anyway! We are playing for fun.
Long live the Pacific War !
Silence over this grave ?
/This post isn't intended to suggest anything to anyone, it's just it's author's a point of view, acquired after several games/