I've noticed something rather odd. When using the Ultimate turbo registers, the manual says not to worry because it automatically sets it to 48mhz. I doesn't appear to do so :P
I ran a level with 30 lemmings and set the release rate to max. It slowed down just as much as if it wasn't switched on (it was, got the blue loading screen). I quit to menu, manually set the speed to 48mhz whilst leaving it on the Ultimate turbo mode and ran the level again. Massively reduced slowdown this time.
Even when set to 64mhz, I've noticed slowdown when all the lemmings are walking along the same scan line (and the sprite flicker is still extremely noticeable). Is this really expected behaviour when running the game with such relatively fast cycles?
Apart from that, great version - really well done to all involved!