Are you using FDISK to change the partition settings??
If so, you may need to use a utility which runs on the same OS as Mandrake. This is due to the incapability of FDISK to read non-dos partitions.
I do not know for sure if this is the problem, since I have no experience with Mandrake, but I have run into this same thing changing drives from an NTFS (Win NT) partition to a dos OS, FDISK (dos version) can not remove NTFS partitions. So, this may be a good thing to think about, try a different utility to remove the old partitions. (look for 'extended' non-dos partitions)
Thanks for the advice, it's very much appreciated.
I was indeed using a DOS version of FDisk, which it appears was not altering the MBR properly - Lilo was partly loading and then freezing the machine. Everything appears to be back to normal now.
For future reference, could either of you recommend a decent partition/format manager? I've got the Partition Magic 6.0 boot disk program - would this be sufficient in future, should I get the chance to revert back to Linux?