virtualbox.org

Has anybody noticed a conflict between VirtualBox and AutoHotkey on a Windows host? It appears that their keyboard hooks can conflict, resulting in AutoHotkey scripts eventually becoming unresponsive (reload required). Other symptoms seem to be modifier keys getting "stuck" in the "down" position, so keypresses end up being alt-keypresses, for example. The clipboard also stops working properly in the virtual environment. These symptoms appear only after a virtual machine has been running a while under heavy use.

The clipboard issue is a known issue and hopefully will be fixed in the next maintenance release.
I am not sure about your other problem as I have not seen it before. If it is directly tied to the clipboard issue I would assume this would be fixed as well in the next release.

I am also seeing the modifier key issue. I've tried to find the reason but haven't, disabled shared clipboard, tried different guest os's (linux 2.4 and 2.6) different win's with same result. It appears randomly for me, it can take days with my guest running (light use on host and guest os) or minutes under heavy use. The only way I have to fix my host stuck modifier key problem is to reboot.

The AutoHotKey problem is still an issue with the current release. I have cross-posted to the AutoHotKey forum as well. Hopefully someone is interested either here or there. Otherwise it is just another annoying cross-compatibility problem.