Hi Kevin,
I did not make any speed changes, but your question made me check the length again and I found the solution for my problem: The length of both clips was the same but since I imported the media in FCP and exported it from there, the timecode changed. The reference movie started at 01:00:00:00 (according to the FCP default). Setting this to 00:00:00:00 and exporting it again solved the issue.
Thanks a lot,
Peter