I'm guessing that means your console is playing the game at 60fps rather than 50fps. I have an NTSC PS2 on which I tried this with FMCB, and the game did run at 60 but wasn't displayed properly. I can also do that artificially on ePSXe, albeit with sound breaking. Here's how it compares (60fps ePSXe on the left vs 50fps Retroarch on the right):

The problem is that the game will only run 50fps on a genuine PAL PS2, so I don't think we'd allow running it at 60 even through a softmodded console (I'm guessing yours is NTSC). Running the game on a PAL PS2 would definitely be fine and would probably be faster than emulator with FDS, the only reason I don't yet is because I only have a PAL PS1.