(Here is a SWAG (Sweet W.A.G.) for you, Mickey!)
Spifldorf,
A quick guess would be that your Outputs are arranged differently on the Mircologix. In other words they are not at the same Slot and Word address as in the SLC 500. Unless you duplicated the I/O type, I/O quantity, I/O card arrangement, slot numbers, and rack size exactly, then your old program will not run without modification.
Many times Sequencer instructions control Output bits directly. If you did not change them in the program to match the Micrologix, it would be a miracle if they worked correctly.
If your Outputs are different, then your Inputs are probably different also, and you may have more problems than just Sequencers.