All Rules is a lot of rules (and is surely going to break something on someones sites, I'm sure). You might want to disable the largest of them to test and see if that's the problem first.
This isn't exactly a cPanel issue, although there are probably more than enough threads on the topic of what rules to use here that you might find some use in, I suggest the docs at gotroot as a better resource worth a peek: http://www.atomicorp.com/wiki/index.php/Atomic_ModSecurity_Rules
Near the bottom of that page you'll find a "Special Note for cPanel users" section.
Also worth a note and you probably are already aware of this, but this is a great tool to have on board as well: ConfigServer ModSecurity Control
The free rules were written for security engineers that know how to tune them for their systems (as are all the free rule out there). If you need out of the box rules written for hosting environments, I recommend you use our real time rules. They were written for hosting environment and non-security experts that just want to install the rules and be done with it. The real time rules are designed with special performance enhancements that the free rules do not have and are tuned for environments like cPanel to ensure that there are no false positives.
The free rules are for security engineers, and you will need to tune them for your needs.