I get the following in the console when the video skips:
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avcodec warning: cannot decode one frame (7 bytes)
avcodec warning: cannot decode one frame (13610 bytes)
avcodec warning: cannot decode one frame (7 bytes)
avcodec warning: cannot decode one frame (15684 bytes)
avcodec warning: cannot decode one frame (2376 bytes)
avcodec warning: cannot decode one frame (7 bytes)
avcodec warning: cannot decode one frame (10695 bytes)
avcodec warning: cannot decode one frame (2296 bytes)
avcodec warning: cannot decode one frame (7 bytes)
avcodec warning: cannot decode one frame (14007 bytes)
a52 debug: emulated sync word (no sync on following frame)
avcodec warning: cannot decode one frame (1294 bytes)
avcodec warning: cannot decode one frame (7 bytes)
avcodec warning: cannot decode one frame (13082 bytes)
avcodec warning: cannot decode one frame (1941 bytes)
avcodec warning: cannot decode one frame (7 bytes)
avcodec warning: cannot decode one frame (14314 bytes)
avcodec warning: cannot decode one frame (1859 bytes)
main warning: late picture skipped (452189 > 0)
main warning: computed PTS is out of range (437757), clearing out
main warning: output PTS is out of range (451757), clearing out
main debug: audio output is starving (251847), playing silence
avcodec warning: cannot decode one frame (7 bytes)
a52 debug: emulated sync word (no sync on following frame)
main warning: buffer is 113625 in advance, triggering downsampling
main warning: audio drift is too big (-138980), clearing out
main warning: timing screwed, stopping resampling
main warning: mixer start isn't output start (-70208)
main debug: audio output is starving (186681), playing silence
main debug: control type=1
EDIT: I was slightly mistaken, and should have known this from the log above. It seems the problem is with the audio codec. I've testing out a few videos now, but it seems that MPEG audio works fine, but A52 (AC3) audio causes the video to skip, with the error posted above.