I named the file exclude.txt I then put it in the AtomicFe main folder and I went into the CFG fiel and told it to use the exclude list.
Ok, i understand better now. you are modyfing the CFG file directly with a text editor.

But be aware if you do that you can have same mismatch if you use again AtomicStudio with that modified files.. AtomicStudio depends a lot on files naming convention. So don't be surprise if some strange behavior occurs.
For the snap problem, it is may be just because the clonelist is not up to date with your mame version.
Try to generate a new clonelist from your mame :
mame -listclones > clonelist.txt
then copy the resulting file clonelist.txt in your project folder (<atomicfe>/projects/<your project>) and also (just to be sure) in the <atomicfe>/metadata folder