Best mod for your tranny is this:
http://www.troyerperformance.com/cgi...P%20-%204R70VB
I am not to familiar with the bully dog programmer but when you adjusted the shift firmness something else may have adjusted with it that you could not adjust and didn't know about. Some programmers are like that out there.
Try it in stock without the programmer and see if it happens. If it still happens in stock then its something in the tranny but if it doesn't happen in stock then its the tune so change you settings back.