Our lab is having some problems with 2nd dimension SDS PAGs. Silver staining of our gels reveals that the proteins are well separated at the top half of the gel. However, they are stacking up at along a mysterious wavy interface before they reach the bottom of the gel. The BPB dye migrates normally, though it is a little diffuse. The gels appear to be set properly and are robust in the staining procedure.
Some people have suggested that a 10x running buffer stock may be the culprit (contains SDS). Others have pointed at a 1.5M tris bottle. Yet another person suggested that the gels were set too fast.
I have had the same problem with 10 or 12% gels cast in a chamber or singly.