I think the issues I am having is because I am trying to split the romsets over multiple paths.
For example one folder for 0.034 and then one for changes to 0.036 and then one for changes to 0.037b5
Although everything may 'look ok to my eyes' with this setup, I have the feeling that Mame (maybe because older versions) and Clrmamepro are not handling the multiple paths to well. I think this could be causing the 'audits' to get messed up.
Is there a 'proper' way to do this or should I not use multiple paths when auditing? I'm starting to think I shouldn't use multiple paths at all.