Hi egirardi,
Turns out that I may need some kind of a sample application after all, as the tracker entry I referenced before has been indirectly fixed during some other fixes in 6.4.0 Release d, so I closed that one down. I did thorough tests on multiple versions of the framework, including JQT and WinWeb, as well as many browsers, and it's fixed alright.
This means that I am unable to reproduce your problem. I even made some changes to the sample application(s) in that tracker entry and had it show Popup on Timer.Tick, but still, the timer fires just like it should.
Please see if you can narrow the problem down to a manageable application that you are able to email to support.
Palli