CC works better before Batch Fixes

Hi, not sure where I should post this but I'm having an issue with Batch Fixes. I have the latest updates to both S4S and the game itself. The issue is that when I run batch fixes, for example Allow CC for random, aliens, mermaids etc, some of my CC ends up no longer available in CAS. It worked fine prior to running the batch fix but now it no longer works. Luckily I keep copies of all the originals in a separate folder, so I just reinstall those files. One example of CC that I'm have an issue with is NotEgain's Nightcrawler tail. Being a comic geek, I have complete teams in my Sims worlds. So this file is essential to my Nightcrawler character. I thought Batch Fixes were supposed to fix issues with CC not break them. So other than having to go through each time I do a fix and replace the damaged "fixed" files with the original's, is there something else I'm missing here?