first, what format is your sequence? I've generally found that you need to massage your sequence before sending to color. Putting everything you want to correct on one track and duplicating your sequence and deleting other tracks. Have you applied any other filters to clips besides the 3way color correct? Any speed changes? Multiclips? Imported graphics?
When I decided to use color to color correct a feature doc a couple of years ago, it took me about a week to clean up the sequence before I was able to successfully send it to color.