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version: 0.9.8 r4600
game: Ar Tonelico (doubt it matters)
After pressing f1, f2 and f3 for some time, I've noticed the program log saves to a different state than what the emulator shows. Example: the program log saves to state 8 but the emulator shows state 0. Most likely the emulator missed a couple f2.
Also, after a while the emulator keeps running the game but ignores any buttons pressed( e.g. esc, f1, f2, etc).

Try with the latest SVN build and disable the "save state # in title" option in Lilypad:
http://forums.pcsx2.net/Thread-SVN-daily...-by-Orphis

there was a somewhat recent fix about it so that should do it.

Also not reading the function keys after a while only happens after changing windows a lot as far as I know and can be fixed by changing the Keyboard API in LilyPad also.

That stop of reading of function keys can also be fixed by saving the game from gui window(althrough not sure why this fixes it).