Hello,
An update:
The issue is now solved. By exporting the master sequence from FCP without lower thirds, I´m able to add the lower thirds in AFX and render out a useable master from there. Exporting files between FCP to AFX needs to be planned very carefully to be successful, it seems. The color shift bug is probably caused by how each software treats RGB vs YUV (AFX vs FCP). The ProRes codec is excellent as long as I stay inside Apple´s world, but not so good if I need to do work outside it. Hopefully this issue will be solved some day? I´ve spent at least two days to find out how to deal with this issue. Workarounds are great, but only if you know of them. Consider yourself warned.
Best,
-terje