(This happened with Version 126.96.36.199. We removed the problem plugin before upgrading to the latest version of NSCloner so we don't know if that update fixes this problem or not. We're not going to reinstall the problem plugin to test it since this is a production machine and we don't want to re-break things.)
The problem as we experienced it:
We are running a WP multi-site install on IIS. When attempting to enter the dashboard of a cloned sited from the Network Admin>Sites screen or directly by typing the /wp-admin at the end of the site url, the whole back-end of the WordPress install locked up until the request timed out with a 500 error. The public side of the sites continued to display correctly.
The back-end of sites made from scratch both before and after the problem started always worked.
Here is an excerpt from the server's Process Monitor while the problem occurred. (https://dl.dropboxusercontent.com/u/42699085/ProcessMonitorWordPressClonedSite.jpg)
Lines 50643, 50646, and 50652 show the lines captured by process monitor that led us to the mobile plugin from websitez.com as causing some kind of problem with the cloned sites; and happily, deleting the plugin solved the problem. That plugin is WP Mobile Detector. (http://wordpress.org/plugins/wp-mobile-detector/)
Also: Line 50665 shows the line captured indicating action created by NSCloner to write to its own log file. Do we know the purpose of that?
Nebraska Library Commission