If you are using the release version of Windows 10 (10240?), the _Timer_GetIdleTime() is indeed reset when using a Game Controller. Microsoft considers this a bug, so...
In the big november update (1511), they fixed this so Game Controllers no longer reset the _Timer_GetIdleTime() (And your screensaver goes on if you are only using a game controller...).
So the reason for my problems was because the BlissBox was sending out a signal every 16ms. With the release version of Windows 10, this reset the _Timer_GetIdleTime() every 16ms. I've updated to Windows 10 version 1511 and the problem is gone.
Of course, now _Timer_GetIdleTime() is pretty useless if you are sitting with a game controller only, but that is not Autoits fault but a design decision from Microsoft.
Turranius got a reaction from careca in Problem in windows 10 "_Timer_GetIdleTime()"