I used CNBr activated Sepharose 4B a lot and I had once the problem you described.
If the concentration of the ligand you want to couple is high, the handling must be carefull. Otherwise it aggregates.
To avoid such precipitates, I incubate the protein wiith Sepharose in the tube with gentle rotation end-over-end, having as little air as possible in the tube.
This should help
Maybe you overloaded the wells. Try to load less proteins. Of course the amount of protein for good separation depands on many factors as thickness of the gel, number of different proteins... but for example when using BioRad system (1mm gel 9x6 cm, 12 wells) I load not more than 30 mg of cellular extract- works perfectly.
In my experience I faced this problem many times. Generaly silver staining is indeed known to be more sensitive than Coomassie however it does not apply for all the proteins. For some proteins you can actually find the opposite.
Unfortunetely besides my own experience, I cannot give you any references.
It depends on the acrylamide concentration. But genaraly the small proteins separate first. Your problem could be that the smallest proteins run out from the gel. Maybe you should run the electrophoresis shorter.
What is the mininal/optimal concentration of proteins for efficient precipitation with TCA? I lose my protein in the precipitation because of too low concentretion and I need to add some extra protein to the solution (I use BSA) but I don't want to overload the SDS gel.