It's possible that your Lr preference file has been corrupted in some way. Try deleting it, restart Lr then reconfigure auto-import. Hopefully, this will fix the problem.
Looks like it was a file naming conflict, oddly enough. When I tether with my Canon 5DMKIII it seems to start the image naming over from scratch anytime I have to restart the EOS utility. That's not normally a problem, but I guess if you get to many img1-* it runs out of unique names or something, so it starts thinking there are duplicates and doesn't import them (and also doesn't error). The manual import actually overwrote files of the same name (without warning me)... which is how I found the problem. Changing the auto import preferences to rename the files on import seems to fix the problem.