I had another issue with RT a while back (validation+custom partial refresh resulted in losing content). Maybe my workaround can work for you as well.
Try to put this in onComplete of the refresh that updates the RT field:
// Process any autogenerated submit listeners
if( XSP._processListeners ){ // Not sure if this is valid in all versions of XPages
XSP._processListeners( XSP.querySubmitListeners, document.forms[0].id );
}
The blogpost:
http://dontpanic82.blogspot.no/2011/02/xpages-richtexteditor-custom-partial.html
If you haven't used onComplete yet, this shows you where to find it:
http://www.domino-weblog.nl/weblogs/domino_blog.nsf/dx/location-of-new-events-in-xpages.htm
Let me know if it works :)