To give you an update:
I have tried /remote off and there are no timers active and I agree that the 30th minute is screaming a timer.
If I use /remote off and relaunch the client without connecting to a server, it will not focus every 30th minute.
I've tried connecting to a single server (Quakenet at first and after that EsperNet) and both triggered a window focus.
I do have perform settings for each server but they mostly contain /msg or something similar but there are no timers and they only execute at connect.
I don't think it's a script issue if the problem still persist after a /remote off + restart and only happens if it's connected to a server.
But I will definitely try a portal install and see what would happen. I'll be in touch!