I've finally seen this happen, and I figured out what it is -- this may not apply to everyone else as I'm on a Mac, but just in case it's a general WoW bug:

My set up is 5 accounts on one Mac Pro, using Spaces to hide the clones (this improves framerate on my main dramatically). I use clonekeys to multiplex key input. If you're not familiar with it, Spaces lets you conveniently hide and show different apps or document windows -- it's perfect for multiboxing and keeping your clone instances out of the way and offscreen.

However there appears to a bug either in clonekeys or WoW itself where it gets confused by the way keyboard focus changes when changing Spaces (note I do not mean WoW character /focus, I mean keyboard focus in the app). Sometimes it gets convinced the control key (every once in a while, shift) is still down after I've released it, probably because control-arrow keys is how I change which Space I'm looking at and key up events may get missed as the Space changes. So I press my auto-run key, which is bound to a /follow macro on all the clones -- but some of the clones see it as ctrl-run, which isn't bound to anything, and thus gets interpreted as the usual run key. Hilarity ensues.

I haven't tried to reproduce this without using Spaces, so I'm not sure where exactly the bug lies. So far I've never seen it in any app other than WoW, so it's either WoW or Clonekeys. Collection quests require a lot of changes to which instance is in front for looting, so grinding Darn rep this weekend I saw it a lot.

Alt-tabbing twice (to focus off/on the main instance of WoW) fixes the "stuck" control key.