Problems running search and replace on multisite database

I'm having problems using interconnectit's search and replace script. I need to make a clone of a multisite installation to hand off to someone (after removing sensitive data). I've made a copy of the site at another location and I'm trying to use the script to update the database to the new url.

It finds the database and tables okay, but when I run the search and replace it tells me that my replace string is empty, even though it isn't. Has anyone run into this issue before and have an idea what problem it might indicate?