You exported then imported and married the imported video to your original audio, right…?
It really looks to me like its audio related. Is it 48k or some weird sample rate? If its not 48k, or FCP thinks its not 48k, FCP might be trying to alter the video to keep sync.
If all appears normal, you might want to try to put the audio tracks into Compressor and re-export as 16 bit/48k and see if it has any effect.