I had a few issues with keyclone crashing but assumed it was due to my crappy comp being unable to handle 5 wows and keyclone with lack of resources leading to one of them closing.

That being said, it did only happen in safe places when I was handing quests in or getting ready to log. I think alot of the time I was switching to one toon to do this (once due to having all bag spaces full, so had to run to the vendor, and the other times to mail items/go and train) and pausing keyclone so I didn't forget it was running and make my alts do crazy things while I wasn't 'watching' them.