Peter, here's a guess:
The ST-E2 communicates information to the other flash units (Canon's flash units that is) via infra red light. Obviously, it communicates all the necessary information to the flashes BEFORE the actual exposure is take. Your strobes are probably getting triggered from the communication info of the ST-E2 and when the shutter finally opens your strobes have already fired.
I've heard of pins being covered to solve the problem. A quick search pulled up this thread over at satan.com:
http://forums.dpreview.com/forums/re...essage=4310266
Perhaps this will lead you in the right direction.