I had a similar problem with and old set of specialized trispokes. I bought some lead tape, the kind they use to balance golf clubs. They're 3/8" x 2" rectangular pieces of lead with an adhesive backing. I always check the balance them with the tire on. A new tire doesn't affect the balance but a worn one will. Since the wheel are clinchers, I was able to stick as many as needed to the concave interior part of the rim. Then I do the extra step of covering the lead pieces with electrical tape over that. Once the tube/tire is inflated, the pressure holds it pressed down on the rim. The good thing about this tape is that it is very maleable (sp?), will contour to the shape of the rim, and can be trimmed with scissors. If one of my tubular Alps was out of balance, then I'd have to stick the lead tape to the outside of the rim where it won't interfere with braking. Thankfully, I haven't ran into this problem yet.
My training rims are way out of balance when spin them, but then I ride them I don't notice anything unusual. So who know if there is a real performance loss. I just like to have equipment that's set up as close to perfect as possible. I should be this anal with my training. That would make the greatest improvement for me personaly. That's just me.
E-Z
--It ain't a good idea to swim near MY bubbles!