I was running FCP 7.03 on a late 2013 MacMini, editing 2K CineForm footage. Initially, I had issues with the watermarks appearing, then I installed the GoPRoStudio software as well as the decoder plugin and was able to render/export without the watermakrs appearing.
Now I am on a late 2013 MacBook Pro. Installed the decoder, as well as the GoProStudio software, and at first was getting the watermarks on the rendered parts. Then they disappeared, but the resulting rendered segment has black horizontal lines all across...?! Attached is an image for reference.
Syatem: macbokpro i7 2 ghz 8gb ram, intel iris pro card, mavericks 10.9.3, Go Pro decoder version 126.96.36.199
FCP really doesn't like editing codecs that aren't it's own. Meaning it loves DV, loves DVCPRO HD and HDV...is enamored with ProRes. But it gets grumpy when working with H.264...Cineform...even DNxHD (Avid's codec). Random issues can arise when not working with FCP codecs....this might be one of them. What might work on one machine, or one day, won't work on the next machine, or next day.
Try this...duplicate the sequence...change the sequence Compressor to ProRes 422...render, then export.