I have a Fanatec csw2.5 wheel, Simworx pedals, and the HE Seq shifter. All work ok for me.
I had to choose Custom Wheel under the Controller menu, then assign all of the axes to my wheel, pedals, and assigned the HE Shifter for gear changes.
I did delete my AMS2 folder from Documents first, since that was advised by Reiza with the latest update release. If I used the Fanatec profile, it will assign the paddle shifters, so I assume you need to start with a totally new profile.