I use custom formats for some rules. For instance, at rule php:S101, I set the format to ^[a-z][_a-zA-Z0-9]*$ instead of ^[A-Z][a-zA-Z0-9]*$
Every time I open PhpStorm, it says my class name does not follow the rule ^[A-Z][a-zA-Z0-9]*$ (and that goes to all my custom formats). If I disable/enable any rule, all warnings go away
The issue appeared to be a bit more concerning than expected. Any modifications to the rules in standalone mode are not considered after a restart, it requires to re-apply the settings. We will provide a fix for the next release; sorry for the inconvenience.