I'm really not sure what happened there. If a) the partition scheme was not changed. b) the boot disk was made in the middle of the current install, c) you booted the boot disk and just pressed the enter key at the boot prompt. d) You installed the system to boot to the graphical gui (level 5)
Then the boot disk should have left you at your graphical login. I know someone that can't modify their MBR because of some compatability software that has to be in the MBR to translate a new disk to an old PC, and that is the way he boots his linux part. He starts it with a boot floppy in a: drive! side note: I recently tried redhat's new beta on this box, and then returned it to Mandrake 8.2 To make a long story short, just for fun, I had the old bootdisk I created in the middle of the rh install. I had not changed the partition table, (just the os) and stuck this disk in and booted to my mandrake gui. Some device drivers didn't load because of the kernal / os difference, but it actually got me to a graphical log in. Linux expects to be on a linux native partition either ext3 the new journalized one or ext2 the old type. The swap should be on a linux swap partition. If a small /boot partition is the first partition made on that drive, then it should become partition 1, like /dev/hdb1 a primary partition. Mine was toggled as bootable. The boot partition is only occupying about 10 megs. (I made it bigger than that however) If your swap partition is next then it will probably be configured as part #5, like /dev/hdb5 (say 300 meg or so) If root (meaning filesystem root or / not the one
named root ) is created next it should be part #6. If you are using the graphical linux disk partitioner from mandrake, a second primary partition should (automatically)be created like /dev/hdb2 which would be an extended type partition, covering the entire space used up by numbers 5 and 6.
you probably would not be able to see hdb2 in the listing of a graphical partitioning program. You would be able to see it in a text based linux prg, like linux fdisk, but that's another story. See I am assuming that you are installing on an empty slave disk, you have chosen to
manually set up the partitions from within the linux install program. I am also asuming that you chose to remove the old unwanted partitions with the partitoning program, and build new ones of the proper type, not try to convert something. After you would do something like this and write the new partition table to disk, the program would show you your new linux partitions and ask you to confirm ones to format for linux. Then the install continues. When installing to a box that has an os like WinMe on the first physical hard drive and I know I will not have quirks or problems if I modify the MBR of that harddrive, then I tell the installer to put the linux bootloader on that MBR. It generally will setup lilo to default to linux as the default image to load, if the other is not selected in the 'countdown time' if the other is not selected during boot. The bootloader can be reconfigured in Mandrakes' control center after you boot up and log in as root. This is the way it worked on my box anyhow

Read the instructions on the screens of the manual partitoning program carefully. Please note you have to select the mount points for the partitions: /boot and / on that screen. As always backup your important data, before proceeding with the install. Happy computing.