I get these glitches as well - not every time though. Also, if you can get as far as the next loading point, it normally clears up again for me at least. I'm using a real CD32, with a 50Mhz TF330. Very impressed overall - amazing effort!
Thanks. Great to hear about the A1200/CD-ROM setup working well.
About the graphic corruption, similar issues were reported on other Scorpion game too, check this post.
Still not 100% clear what exactly causes it, but it's worth to mention that I never got reports of graphic corruption coming from the standard A1200/A4000 version (non-CD), so, there's that to consider too.