@derekr resizing to 512x512 seems to have fixed a lot of the issues. Another one that I came across was that the ".PNG" extension of a couple of my files was capitalized. Make sure that your files use the lowercase ".png" extension.
Aha! I see it was failing to find the BIOS - I didn't consider that because literally every other game has worked perfectly. dc_boot.bin and dc_flash.bin were both in there, but they were the wrong files. Have now replaced them and everything's peachy. Cheers for the tip :)
@mitu - Thanks a lot for the reply. I was pretty concerned this was a config setting I had stepped on somewhere. Sounds like it is just something I will have to deal with for now and maybe a future Flycast or Retropie build will address it.
-Sega Rally - Ran great
-Kiss Psycho Cirus - Ran around in the first room but seemed to be fine!
-Puzzle Bobble 4 - Playable but with a bit of slow down (it seems so simple too...)
-Super Runabout - Seemed to be full speed but with intermittent stutter.
@greenhawk84 Sorry currently my pc has broken down so i backed up Retropie and installed Raspbean so i could continue to work from the home office, so all i got left for gaming momentarily is my RPI0 which i turned into a Sega mini :-(