@Critz :
Sorry for the time I took to answer, but I did a lot of tests.
So I tried on 2 different versions on Windows 8.1 (english x86, and french x64), each time with lots of different game versions (v1.02 jp, v1.10c jp, v1.21 jp, v1.31 jp, v1.33 jp and v1.33 with english patch v1.02a)The windows were empty, installed just before the tests, with only directX and the graphic drivers. And for each test, with every version, I had your bug while using Alt+enter 3 times.
Therefore, the bug isn't related to the english patch.
Also, I don't know why you hadn't this problem with the japanese version. I only have a small idea, this may be because the patch still uses some parts of the version 1.21, and don't have some optimizations added later. And if that's it, the graphic card used may change something. If you want to try, I can send you a copy of the game v1.21, through a private message.