I have not been able to reproduce the button highlight issue so far. I used the following script to monitor activation events:

on 1:APPACTIVE:echo APPACTIVE appactive: $appactive
on 1:ACTIVE:*:echo ACTIVE active: $active

mIRC should always show the above events when it is activated and deactivated - they are directly linked to the way highlighting works.

If you use the above script, do you notice any difference in triggered events in the two situations that you described?

Can you describe a step by step method that reproduces it for you that I can use to reproduce it here?