The molecule SDS is an anionic tenside and should dock to the proteins with its lipophylic tail.
Basic proteins are charged positively and though the SDS-molecule dock with its negative head - the sulfate group - to the proteins.
This will not enhance the negative charges of this mycelles which leads to a bad behavior in SDS-electrophoresis.
Remedy is to change to a TRIS-based buffer-system (ElphoGels) or, the best:
Run a native cathodic electrophoresis (native cathoda buffer kit, DryGel Elpho)
Please note that basic proteins will like this applied acidic buffer system....