I have had trouble getting a sim to stop running. I started up a custom batch swapping in all the legendaries (including the new 7.2.5 ones), but forgot to change the sim version to 7.2.5, so I think it's probably hung up somewhere on a new spell interaction or something. I used the Clear Queue command in the client, but the sim seems to be pretty stubborn, and keep restarting when I reboot the client. This happened last week on a different sim, but that time it was resolved by a new client version releasing and invalidating the queued simulation.
The sim in question is http://www.askmrrobot.com/wow/simulator/report/836fcf12f45540d7bf9a00b0201e8489