So while running PCSX rearmed on the Vita I found for some FPSs I needed to map the L1 R1 buttons to do strafe. I went into the control configuration screen and set up the L1 and r1 (basically flipped the default) and mapped the previous functions that were on the shoulder buttons to the analog stick as they were just menu functions in this particular game.
What happened was the R1 button mapped fine but L1 did not remap. It just stayed as it was default. I tried a couple of times exiting RA etc but no luck, L1 refuses to remap.