Have you found out if they were being merged or selected?
I often use vertex snapping + auto merge, and would be quite interested in a way to auto merge on demand.. With automerge I try to keep it disabled most of the time, for fear of accidentally merging things..
AARGH, I thought I discovered something and now after pressing auto-merge on and off again I can't tell. BUt I found the image that I used showing the original settings.
Auto-merge wasn't active but after snapping, LMB, Shift RMB they got merged.
Was this a (unintended) hoax and I should delete or did work? I used 2.72a