I don't think it has anything to do with the anti-hack. Is your web browser Firefox? I recall there being an issue with dragging around windows or using Firefox before with hardware acceleration enabled for some people and it has nothing to do with anything we've done in particular.
I think it needs to be said that crashes are going to happen. BB didn't even allow Window mode when it came out and the game can still crash when transistioning the BGM 15 years later. BB ran like shit when it was released (compared to other games at the time) and ST never worked on that. On top of that, the game is pretty fickle, just by looking at what we've seen on the forum.
I still haven't gotten any crashes with Firefox in the background, and I also tend to drag my windows (including BB) to other monitors. But if something starts flashing on my taskbar, the game tends to shit itself.