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Not sure about DRM protection, but I have had issues with videos from iTunes. Typically I have to run them through Handbrake to recode them to MP4 format instead of iTune's m4v.
You should be able to just open them in MPEG Streamclip, and do a "save as..." MP4.
That way you're not re-encoding (and degrading) the audio and video, just putting them in a new MP4 container.
If Apple has started DRM-ing their music videos (again) that's too bad. But they were always a last resort in terms of quality anyway.