@SpudsMcToole Hm.
Any competing bluetooth devices? You seem to mention another dongle of sorts.
Have you tried the instructions here
https://github.com/RetroPie/RetroPie-Setup/wiki/PS3-Controller
for "older versions of RetroPie"?
Also, in the guide, it clearly states "Note: Do not enable other bluetooth options as these will conflict with the PS3 specific bluetooth setup (sixad)", so I wonder if you have any competing bluetooth service turning on, regardless of dongles and stuff.
I'd try going through that guide, extensively, and seeing if anything works - and yes, disconnecting any other Bluetooth device (and potentially uninstalling any other bluetooth service you might have started or enabled unknowingly).