The pinentry-qt dialog appears when a PIN is needed for SSH authentication. However, this does not grab input focus, and appears at the end of the ALT-TAB menu. While the `grab` option is set in `gpg-agent.conf`, it doesn't seem to have any effect.
Edit by @aheinecke:
This has been reported and noticed also in other circumstances. We have code in pinentry-qt that tries to pop up in the foreground. On Windows the operating system does not support this properly, so we use hacks. Those hacks do not always work and need more work. Strangely enough the way GTK-2 does it seems to work, but trying to copy that behavior for Qt did not work properly.