Ajax error with clean urls

I moved my site to another folder and everything is working great. However, I noticed that in firefox and IE, Homebox is bringing up an Ajax error when moving a box:

An AJAX HTTP error occurred.
HTTP Result Code: 200
Debugging information follows.
Path: /system/ajax
StatusText: OK
ResponseText:

This error did not happen before I moved the site to a new folder. I cleared the cache - still no luck.
I then decided to turn off clean urls. The error went away. I turned cleaned urls back on and the error is back.

Any idea what function homebox has with clean urls that could be the cause of this error?