Just to make sure. When the flex joints were installed, were the pilots installed into the trans / drive shaft flanges? If the joint isn't clocked properly things won't be held on center. I quick check would be to look at the joint / flange interface for seating. Then under the bolt head to make sure the pilot isn't under the bolt.

When I did the same change out on my 97 C280, it developed a fast ( drive shaft speed ) thrumming feeling at specific a speed. My center u joint is notchy and the new center bearing mount would have moved things a bit causing the joint to go in and out of notch.