I have kanotix installed to hard drive and it came with grub-gfxboot installed.
It's been working fine but on a whim I decided to remove it and install
regular grub so I could use my custom grubsplash.
I removed gfxboot first, then removed my /boot/grub directory then installed grub and did update-grub to let it generate a menu.lst.
I then edited menu.lst and ran grub-install.
After rebooting I am presented with a grub prompt and nothing else. I don't know what I've done wrong since I've removed lilo and installed grub the same way before with no problems.
I installed grub to my root partiton where grub-gfxboot was installed and it is chainloaded from another primary grub on the mbr.
I have been through my menu.lst very carefully and can't find any problems with that.
Could grub-gfxboot have left something behind that is interfering?

Another thing, this happened with both gfboot and now with regular grub - when I do update-grub it keeps removing my other custom entries
which it doesn't do on any other distros.

OK, you have replaced the copy of GRUB package installed by kanotix by another GRUB package you got from elsewhere. Hmm.. doesn't make sense why would you do so. As far as installing your own grubsplash is concerned, you could do it without uninstalling the distro's GRUB package ! All you needed was the gfxboot package. Even with currently installed GRUB, you are going to need gfxboot package !

You need to understand and differentiate between GRUB package install and GRUB bootloader install. What you installed was a GRUB package install followed by re-installation of GRUB boot loader which, gets written to the MBR and boot (or other) partition.

If booting displays GRUB prompt and there're no error messages, GRUB probably cannot find menu.lst. Are you sure, you do have menu.lst under /boot/grub/ directory and its contents are correct.

If you are not sure, post the contents of /boot/grub/menu.lst and the out put of command "fdisk -l /dev/hda". Make sure, you replace hda with whatever disk device file you have/are using.

EDIT: I missed a word here and there while reading thru' your post, the first time. You say, you uninstalled a GRUB with gfxboot support and replaced it with a GRUB without gfxboot ??!!&^&*(*& And, yet wanna use a custom grubsplash ??! gfxboot is what GRUB uses to display grubsplash !! Er.. !!#$

I removed the kanotix grub-gfxboot and replaced it with the debian sid regular grub (kanotix is basically debian sid once installed).
The custom grubsplash I'm wanting to use is a .xpm.gz image in the grub directory and is different thing from the splash used in grub-gfxboot and, according to a script I used to check compatiblity with the grubsplash, gfxboot isn't compatible with .xpm.gz grubsplash.
I also wanted to try regular grub to see if that was the reason my custom entries kept being removed.
Incidentally, I've worked out why they were being removed now so that's no longer an issue.

I have suse's grub installed to the mbr and use chainloader entries in that to point to other distros, which have their grubs installed to their own root partitions, this is so I don't have to keep updating suse's grub everytime a kernel is upgraded on one of the other distros.

My menu.lst

I've copied the actual boot options from this menu.lst into suse's grub temporarily and it boots fine so there is no problem with those.