I’ve just been doing some research on HDV, does this sound like it might be the problem?
As a consequence of the fact that HDV uses the interframe MPEG-2 GOP (group of pictures) structure instead of a solely intraframe compression system, native editing of HDV footage differs technically from the native editing of DV footage. In DV, frame-accurate splicing does not disturb the surrounding video because each frame of the video is stored as a self-contained unit. In HDV, splicing always introduces distortion at the splice points, due to the interdependencies between groups of video frames. Any editing of the video, whether it be a complex transition or a simple scene-change, requires a decompression and recompression of the entire HDV frame group. All modern professional non-linear editing software handles HDV by recompressing only in scenes where absolutely necessary, rather than needlessly recompressing the entire video. This limits degradation to the points of edit.
If HDV footage is converted (known as ‘Transcoding’) to a good intermediate format for editing, these considerations will not necessarily apply, and gradual degradation from generation to generation of edit may be avoided while substantial system performance gains are made. The lossy Apple Intermediate Codec (which runs out of QuickTime) is an efficient, easily usable codec for editing HDV in systems such as Final Cut Pro but lacks the transcoding and generational quality of some third-party HDV Intermediate codecs
I believe there is an apple codec for HDV that you can convert to that might solve your problem. I found this information on Wikipedia.