in these versions of FBA there still is that "in-built" 1 frame of input delay
here is the fix by
0746:
http://pastebin.com/f1e740bfeand a little description of what it consists of:
[19:59] <Shinta> yeah. Instead of changing vblank interrupt trigger position, I moved the lines for drawing to later in the frame
to test this:
1. open a CPS2 game like SFA2
2. press F2 and select Input from the Service menu
3. pause the game with Pause button
4. hold a punch/kick and press F1 to advance frame by frame
input indicator should react at the first frame