I experienced considerable flex when carrying rear panniers only on my Trek 520, enough to be disconcerting when descending bumpy, potholed and curvy backroads. Besides frame flex I also suspected that flex in my rear rack was making a contribution, but definitely putting weight behind the rear axle will exacerbate any flex issues in a frame. The flex was still there but not nearly as bad when loaded evenly front and rear as the bike was designed. Very comfortable, controllable and a good compromise with unloaded comfort.

I eventually moved to a Cannondale T2000 and as others have mentioned it is a dream when loaded.