I've got this problem too, in infopath 2007.
I've many repeating sections and repeating table with conditional formating.
When I work on it, the conditional formating are "mixed". They aren't in the good repeating section..it's a big mess, and it happens all the time.
I've seen in the xsl of the view the list of the conditional formatings...
The conditions are ok, but the "reference" to their owner change every time!!!
Do you know where it come frome? Do you have a solution?
Thank you