Ok. Slaps forehead. Think I see what's going on now.
When I originally built the kernel I probably pointed it at the linux_1c20.ptf supplied with uClinux to build, but in reality was using the altera supplied "standard" configuration, that's the only explanation I can see as the altera quartus projects don't actually have the compact flash interface enabled. Time to disable it the kernel and try again.
That also explains why I was never able to get the compact flash interface to work in uClinux!
Maybe we should have a sticky thread on the board of things that we've found out, i.e lcd not working if compact flash card is inserted, kernel cleaning, altera projects not having compact flash enabled, etc.
Once again, many thanks!
Adrian