Some of my source footage was created in After Effects. It turns out that there were a couple of cue points in the AE comp that had similar names to the cue points in Premiere - the AE comp was saved out to an AVI (with metadata enabled I think).
Premiere wasn't seeing this metadata and the cue points, but Media Encoder was (and it couldn't be deleted in ME - just kept coming back).
So - moral of the story - be careful with metadata!!!