I'm an audio engineer, who's pretty new to video. My friend and I shot 2 cameras at a concert. His was on miniDV and captured fine into Final Cut.
Mine was a (borrowed) Sony DCR-SR42, which records to internal hard disk. I pulled the video off the camera, and had to use Compressor to convert it to 29.97 DV spec to match the other camera's captured format. It was at 30fps for some reason.
Everything looks ok inside Final Cut and also the exported Quicktime Final Cut Pro Movie file. However, when I use Compressor to encode it to MPEG2 for DVD, the DCR-SR42 footage looks terrible, while the other camera's footage looks fine. The DCR-SR42 looks like strobing interlaced madness.
I don't understand how it can look fine in the exported FCPM file, but then look so different after the encode - and I mean it's basically unwatchable.
Do you have video mixed from both camcorders in the final timeline? If so, keep in mind that they probably have different field-order (the hard-drive cam is upper field first, and the miniDV cam is lower field first).