I'm using RetroPie 2.6, with a DualShock 3 using Bluetooth. I didn't configure any of the retroarch.cfg files as I was under the impression that the input config file was automatically selected. I did just now try copying the input info into the snes retroarch.cfg file but still nothing.
Is there an easy way to upgrade to 3.0 Beta 4?
You should be able to configure the controls via the retropie menu, there is a retroarch configuration option there.
In retropie 3 beta 3 and above this is done automatically when you configure your controller in emulationstation the first time.
I think you can upgrade from the retropie menu, choose the use latest binaries option, however use caution and make sure you have a backup ....
You might be best to just start again but use the latest retropie version, setup is now pretty easy and painless