Dear Kerim,
yes, you’re right. This is indeed not the pattern I expected. Your example does not make any sense at all. However, you can try to adjust all y coordinates to an even Y coordinate (no need to adjust the pictures, this was never necessary in my case).
The Y coordinate adjustment worked for *every* of my problems and it matches the statements in spumux. Probably your case is directly related to FAB and the way FAB organizes subs.
However, I still think it must be related to the Y coordinates. If you convert to avi and some mpeg4 codec there is sometimes a problem if the y height cannot be divided by 4, 8 or something like that. Maybe you can experiment with that idea.
best wishes and good luck,
leo