Recurring audio distortion

Hi all,
I am currently editing a series of videos (for a college lectures series - all the clips are copyrighted and commercial, but fall within educational fair use). Each video combines clips from films along with a commentary track recorded in our audio studio.

I have been running into a problem of audio (and sometimes accompanying video) distortion within some of the clips, as demonstrated in the attached exported clip (this isn't uploading for some reason...) The original media that FCPX is linking to is fine, and the clips all play fine in the event browser. When I place a clip in the timeline, it starts out fine. At some point in the process (it doesn't seem to be connected to a particular action on my part), I will go back to review a section of my project and the clip will have become distorted. There is a workaround - manually replacing the clip with a duplicate from the event browser - but I have to constantly review finished bits of the project in case bits of it have changed behind me. The project is 14 hour+ videos, so this is onerous to say the least.

It doesn't happen with every clip (30-40%), and I can't identify what is causing it. The DVDs I'm capturing are pretty various… some blu-ray, some not (both have become distorted), widescreen and standard (again, both have become distorted). They are captured in iMovie and imported directly into FCPX as DVs, without any iMovie export.

Some example specs, based on the Quicktime inspector readout:
TOP HAT original: DV, 720 × 480 (640 × 480), Millions
DV, Stereo, 48.000 kHz

HUGO droplet converted: Apple ProRes 422, 854 x 480
Linear PCM, 16 bit big-endian signed integer, 48000 Hz, Stereo (L R)

AUDIO: Linear PCM, 16 bit little-endian signed integer, 2 channels, 48000 Hz

At first we thought it was because the audio commentary was an mp3. Re-recorded as a wav; no luck. Thought it might be a frequency issue… some of the clips were 32 kHz (though it wasn't only those that were having issues). Converted everything to 48 kHz using the Compressor (the HUGO specs are post conversion, the ProRes 422), same issue. Thought it might be a codec problem with the audio commentary being Linear PCM and the clip audio not matching, but at least one of the files having problems was Linear PCM. Gave up.

Has anyone encountered this sort of distortion before, or have any thoughts as to what might be causing them? I can hunt down more specs/settings if anyone needs them.

Thanks in advance!

It would be helpful if you could upload some examples. "Distortion" could mean one thing to me and something entirely different to you. Where are your media files stored?

Sorry - tried to attach the example to the initial post and it wasn't working for whatever reason. I'm going to try to put the exported example on Google Drive.

docs.google.com/file/d/0B06tu5bqTrRwVWwwejJJRVhPSmc/edit

Is this viewable?

I'm wondering, do you have your import settings set to automatically fix your audio? I keep this turned off. Perhaps it's trying to fix something that isn't broken.

I've had good luck importing video from dvds using Handbrake, and then editing the mp4 file into my project. You can select specific chapter ranges to convert as well.