Please don't take offence at this, but it's the silly things that trip us up when we forget about them.
U-Boot will load Kickstart from the first partition it sees. If you have two or three "Bootable" partitions on the one disk, then Kickstart will be loaded from the first one, no matter how old it is.
Once Kickstart has been loaded, the OS4 System will be booted (that is, Startup-sequence will be read and libraries loaded from) the bootable partition with the highest boot priority.
It is quite likely that you are reading Kickstart modules from one partition and loading libraries etc from another. It might have been running that way for a long while - if you have two or more partitions with very similar Kickstart directories, you would not even notice.
For safety, the new partition on which you have installed OS4 should be the ONLY Bootable partition on that drive. Using MTB, switch off the "Bootable" flag on every other partition. You can still boot from the CD and run MTB from there to make changes.