I do a lot of multiclip editing and do have the same problem. However this color glitch problem only occurs on those clips were color correction has taken place. When i remove all filters from these clips, the glitches after export are gone but the end movie result is bad due to the difference in color and other filter settings.
To me, and please correct me if i am wrong, it looks like these glitches only occur after having the project moved, copied or made smaller for eciting purpose. With the orininal capture footage on its original place, i have never had any problems with color glitches after color correcting and exporting.
FCP 7, MacPro 8core 3mhz, 8Gb intern. Nvidia FX 4500, OSX 10.6 Snow leopard.