I use gpg-agent with ssh support to make using passphrase-protected keys easier. The pinentry program I have been using is pinentry-qt4, but when the pinentry box pops up it 1) appears behind other apps, causing me to have to switch to the pinentry window, and 2) doesn't return focus once the passphrase has been entered. This results in no window being set as the active window, which breaks Alt+Tab application switching (the application switcher just says "No Windows" on it). Hitting Alt+F1 to bring up the KDE menu and then closing the menu will return focus to a window, giving me back my Alt+Tab functionality.

These problems occur irrespective of whether or not compositing is enabled.

In the meantime I have switched to using pinentry-gtk-2, and neither of the behaviors described above occur. I'm using the oxygen-gtk theme so there's not much of a difference in how the pinentry window looks, but I would prefer to use pinentry-qt4 as it is "prettier" that way.

Is the same thing happening to anyone else? If not, any ideas on what can be done to troubleshoot it?

IIRC this is a known bug. I don't observe it with most recent KDEPIM versions, but there is no stable release for them yet.

OK cool, at least it's nothing I'm doing wrong, then.