That means pcsx2 didn't install properly. Try re-installing and then look in the last log file under $HOME/RetroPie-Setup/logs to see if there are any errors related to the installation.

@X_Splinter said in Unable to use keyboard/controller after rebuild boot partition:

Could this be an issue not related to the boot partition?

Most likely yes. The procedure you performed is not guaranteed to recover another system.

If so is the main partition of retropie a regular EXT3? So I may browse and copy all of my files?

It's an Ext4 partition - should be accessible also as Ext3, but I advise using a Linux installation to try and mount it.

@jonnykesh I haven't yet, I will try later on tonight