To be honest I would have to see the whole event sheet to see if variables are being reset or not.
I use the built timer extensively in my game, as matter of fact, I have 3 of them running on one layout without issues in both the c2 and c3 runtimes.
I certainly can help more if you could create a simple project that reproduces the issue, if you don't want to share this one, and provide a link to it via drop box, one drive, etc....
I would be more than willing to look into it more