Yes, it happens with other windows as well. It’s a known problem, at least. 
– Thomas Adam
I’ve noticed when this problem occurs for me under firefox, that if I move the mouse over some gtk text input box of another app and then back to firefox that it appropriately takes focus again… and that’s using SloppyFocus.
Yes, gtk applications especially exhibit this. It’s being looked into, I assure you.
– Thomas Adam