Whatever is producing the popup seems to be running in the background on your machine. Before fixing, or turning it off, you need to identify exactly what it is.
Did you install anything when you were trying to get things working? Any software connected with the Android? Next time you see the popup, try going straight into task manager (right click on taskbar, select Task Manager) With a bit of luck it will appear near the top in either Apps or Background Processes.
Another way of identifying it is to look at the left hand column in Task Manager. It's a menu that lists "Processes, Performance, App History, Startup Apps ......" and so on. Click on Startup Apps and check what's in the list. There should be no more than three or four Startup apps enabled. See if anything looks likely and disable it by right clicking - Disable.
I'll leave it there for now, while you still have your sanity. But remember - it probably wont be hard to disable it, but first you need to know what's causing it. 
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