Hinson wrote in post #4744212
Ok, tried it and have the same problem but in a better way. With tape covering the 4 pins on the 5d hotshoe, the ST-E2 will still fire the 540EZ but now it's in sync with the camera. Of course this is manual mode only.
Oops! Sorry, I missed the part about you also wanting to use your 550EX in the set up. 
Let me rewind and start from the beginning. If you want to use the 550EX in ETTL mode controlled by the ST-E2, you will not be able to use the 540EZ in the mix using the Wein optical trigger because of the preflash emitted by the 550EX. You might be able to get away with it if you use the Wein "smart" optical trigger which supposedly can be made to ignore the preflash but I have no personal experience with any of the "smart" triggers.
I don't think "hiding" the 540EZ from the ST-E2 is going to help either because the 550EX also emits a preflash. Of course, you can hide the 540EZ from the 550EX, too, but then there would be no sense in having the 540EZ in the setup in the first place. 
You can try the "tape" trick I mentioned earlier but then, the 550EX would need to be operated in manual mode, too.