Blender seems to be interlacing my footage in the tracker/video editor, but nowhere else does it look like that, even if I make blender render it through the sequence editor.
This footage is impossible to track this way.
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You can use AviSynth to deinterlace your footage before using it in Blender on the fly. You can mount your avs Scripts with avfs and Pismo File Mount to have virtual avi files that you can import into Blender.
I use it all the time and it works well, even though it's a bit tricky to set up... Depending on your footage you might need a proper VideoSource Plugin for AviSynth like L-Smash and if you don't want to use the included Bob Deinterlace Filter, maybe use QtGMC.