Problem- Machine zero off after ATC

[MightComet]

We have recently been trying to get a Mighty Comet VMC 1000 with a Mitsubishi 520M control upgrade up and running from a parameter loss. We have matched all the parameters to the hard copy from 1994 after upgrade and almost everything is working like expected. The last major problem we we have is after a tool change the machine zero is off-set by the exact amount the machine went up to change tools.

Example:
Machine code runs fine.
T18 M06;
Machine code runs fine 4.5672" above part (exact amount the machine went up to go to g30 for tool change)

Machine code runs fine.
T18 M06;
T19 M06;
Machine code runs fine 9.1344" above part (exact amount the machine went up to do 2 tool changes)

If you call a M06 and do not change too (called for same tool in spindle) the machine works properly.

When you go to the machine coordinate monitoring after a ATC the Machine height reads like the G28 zero was raised by the 4.5672" amount.

The code is in all absolute, and a G90 is right after the tool change has no effect. From the best I can tell the entire tool change is in the ladder and not a macro like most machines, and it looks like the machine is a re-branded Hartford HV-50s when it comes to bit select parameters.

Please help our guide if you have any ideas of things to try!