In the intrest of full disclosure, my electrical experience is primarily with 1 and 3 phase ungrounded marine electrical systems. Sometimes it takes me a bit to switch back to household wiring.
First off, what is on the circuit? In my limited experience with GFCI receptacles, I think that you would want your lights to be on the LINE side of the GFCI. I would hate for you to be in the shop and have your lights go out if the GFCI tripped.
Are the lights fluorescent or incandescent? If you've got a voltage drop, you may not be able to get some of the energy efficient ballasts to kick on. One of my former ships (now razor blades) had 106v on the lighting circuit. Only the big, old ballasts would excite the light bulbs. But I digress.
That being said, either the GFCI or something in your wiring is preventing the lamps from seeing the full 120vac. If you can, move the lights to the line side of the GFCI, this should eliminate it as the problem. If that doesn't work, check your wiring. Attached is a page with a bunch of different wiring diagrams for 3 way circuits.
As always, make sure every thing is isolated before you start poking around in it, and if you're uncomfortable with what you're doing seek professional advice.
Hopefully, Cassandra will see this post, she's usually got the answers for electrical stuff. Installing A 3-way Switch With Wiring Diagrams - The Home Improvement Web Directory