I was having trouble with iRite munging URLs in links I had created. I clicked around on the checkboxes in the Formatting tab and that fixed it. I'm still not sure what was causing the issue, but it doesn't do it anymore.
As a wild-*ss guess your issue may have something to do with the "Clean WYSIWYG code" box on the Formatting tab and the "Source" control in the iRite window (then again, it may not). Wish I could be more definate, but I'm just learning to use configure it as well.