ClrMAMEPro can be really confusing to get working. It took me ages playing around with it the first time to make it work, but once worked out it is not too hard to use, although definitely not intuitive. I found a good tutorial in how to use it a long time ago and that really helped me work it out.

I could always burn you a copy of the new set and post it to you so you have an up to date copy to start again with?