We shot a 1 hour movie in HDV and cut it in final cut. Everything is cool, timeline plays great.
Tried to export through compressor. Bad news. Six scenes in the opening sequence have problems (over and over) These scenes have effects on them (speed change, desaturate and resize... nothing fancy) Once compressor finishes (which takes 6 hours) and I play the MV2 it created (which I need for studio pro) the scenes mentioned begin playing when the movie gets to them, then they freeze frame until the scene ends. In one case, the scene plays, then turns pink and freezes.
You don't mention at all what your Compressor settings are, nor which version you're using.
I would recommend that you do your final timeline render in 8 or 10 bit uncompressed or ProRes. Export that as self contained and import that into compressor. You can try reference but you're less likely to bump into issues if the file is self contained.
If you are having issues with specific scenes you might want to add compression markers in those areas in FCP to force I frames.
I concure with Craig, but I'd recommend ProRes over the SD formats. The other thing I'd try is changing the render control in user preferences from "same as codec" to "ProRes 422" and re-render. HDV is a quirky format because it's so compressed. Hope that helps.