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Ahh well we finally get down to brass tacks. For anything + softsubs, the best way would would be to just use DirectShowSource in an AviSynth script and capture the frame right out of VirtualDub. Paste to your friend MSPaint, then File->Save As .png. Voila! Nothing out of the ordinary for video editing. Not to mention that makes it exceedingly simple to locate the same frame in both comparisons. Judge by motion in the frame or if its the beginning of a scene, that makes it really simple.
For anything which doesn't require softsubs I would highly recommend using ffdshow's frame Grab feature. It will take the frame directly from the decoder thus no interference from the video renderer, which can be particularly nasty if you use some of the VMR renderers (depending on the settings in your drivers). Plus if you tick HQ RGB (in Output) you'll get a slightly nicer frame grab (this won't effect normal playback though so no worries).
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