I have been having a few issues getting PS2 games to work. I'm on the latest CFW Rebug and the only way they seem to work is by including their config file. I'm sure this was not needed previously. Is that right? Or am I missing something?

What games? A lot of games do need cfg files to work. Here is the compatibility list.
https://www.psdevwiki.com/ps3/PS2_Classics_Emulator_Compatibility_List
You can install ManaGunz and when you load a PS2 game it will tell you if it needs a cfg and it will load it for you and then you never have to mess with that games cfg again. It's easier than installing the cfgs yourself. As you can see by the compatibility list though not all games work and they may never work.