Sorry Chris, but my experience is quite different.
In all of my programs I have a timer in the main callback; its callback at least updates a clock on the panel and blinks a led to make evident the program is active.
This timer remains active when the system popup panels are displayed. Look at the sample project I attach for an example of it.
Anyway, yesterday I wasn't able to reproduce during all day the problem I suffered last week, so I assume the timer disabling depends on some bug in my application and not on a strange interaction between Windows and CVI.
I will investigate more and more.
Thank you for your answer.
Roberto