I always hit skip on the softwarelist when doing the MAME ROM's sets.
Here what I do. I drop the hash\(name of the system).xml into the clrmamepro profile window. Not loading the MAME at all. Just the *.xml file alone.
A lot easier than messing with MAME ROM's + softwarelist ROM's at the same time. It really is BS trying to do both and then you have to mess with all the other BS setups.
MAME and softwarelist shouldn't be loading at the same time anyway on the clrmamepro unless you want to mess with all the paths. Ronan should warn people about this.