Jorahdas,
This is very frustrating for you. I noticed that my USB Saitek trim wheel was causing pauses when I operated it for the first time after the simulator had loaded. After the SU5 update, the pause had extended to around a minute! After the hot-fix, I returned to a 4 second pause.
I have found a work-around for this annoying problem which has lead to one CTD recently…
When/after I press ‘Fly’ I move my Saitek trim wheel backward and forward during the loading phase. No more pauses in the simulator when I operate the trim wheel now! I now move all my USB controllers during this loading phase however, it has only been the trim wheel causing the problems and one CTD when I used it for the first time after the simulator had loaded.
I have just discovered that moving my USB controllers during the first/initial loading phase of the simulator a CTD occurs, (Super Cub and Rhino image). This does not happen if moving my USB controllers after pressing ‘FLY’.
Solution for me: dont fiddle with my controllers during the first loading phase of the simulator! 
I wonder sometimes if some people who are having CTD’s, may have manually edited or changed some of the default files before the SU5 update and if this could be a possible issue for some people too, making a change that is not compatible with this latest rendition of the simulator, (or a change that MIGHT stop a file being over written during an update). I would not assume that such changes would be over written by the update, (perhaps?).
Charles.