Hi Sebastiaan
One possible cause for this is that it sounds like the old FCP - Color round tripping bug that was in pretty much every version of Color pre 1.5.1
If your FCP sequence contains slo-mo, speed-ups, freeze frames, variable frame rates, still images, slug - in fact anything that was not a standard QT movie playing at normal speed, Color would render out a single frame.
Pre the latest version we would have to do what was known as "baking".
Where every shot that was slo-mo etc etc was exported as a quicktime and re-imported and replaced on the FCP timeline before sending to Color.
This turned every shot into a "standard quicktime" file and Color was happy.
The ProApps updates for FCP Studio to Color 1.5.3 are still available as a free download from the Apple FCP support pages.
I would suggest you update if you can and you should not have this issue anymore.
best wishes
Neil
http://www.patience.tv