I can reproduce it with few apps (mousepad, firefox, claws-mail).
For example with firefox when I scroll fast through a webpage, it suddenly stops scrolling and doesn't respond to mouse events until I press any key on my keyboard, it then processes all delayed mouse events along with key press.
When I comment out #define HAVE_XI2 1 in config.h everything behaves normally.
Bisected down to:
Maybe related is bug #14695. Can you try the proposed patch if it fixes this too?
I can confirm that patch in #14695 fixes problem for me.
*** This bug has been marked as a duplicate of bug 14695 ***