Hi Timothy,
This sounds like a known problem we had in some versions of 2012 R2 (and prior). We did wind up fixing this particular search/replace issue in January of this year, so you'll need to make sure you're using the latest version of 2012 R2 (click on Tools / Check for Updates) or CC 2013 for this functionality.
If you're interested, you can find the release notes here:
http://www.casecomplete.com/ReleaseHistory.aspx?currel=2012%20R2
If you've got version 7.2.4757 or later, you should have the fix and we may need to do some digging to find out what's going wrong.
Thanks!
Jason