Apologies for the lack of reply here. Were you able to contact Support to get this figured out? This is definitely not a known issue, we would require a controlled scan test and verbose logs to troubleshoot this.
What I can tell you, we have a timeout in the operations monitor and you will see that error if the scan exceeds that timeout. I'd be surprised if the scan didn't complete in the background, the result would show in Results view. (ctrl+shift+r) We do have an engineering build that allows you to increase the operations timeout, but that wouldn't help with the underlying issue of the slow scan after installing IIS.