If you find problems like you did, don't render h.264 directly from AEt, try to render uncompressed first. When your rendering stops again, you'll have everything rendered out until the moment it stops and can start a new render from that position, and later put the fragments together in your NLE and output to h.264. If it stops every 3 frames that doesn't make sense of course but I guess it's every now and then in the timeline?!
Never worked with XDCAm, sorry. If all fails, render the edit from FCP to Prores or DNxHD or other lossless format and use it in the AE project instead of the original files. If you worked with adjustment layers it should be quick to do. Did you already try to render to a different codec or uncompressed from AE?
