It rather looks like the Shopbot Techs have given up, so I am on my own.
I get the feeling that they do not sell many indexers for the Desktop Max, so making software work for this combination is not a priority.

It appears that I can make it work by having a different cut program for each different tool I use, and edit each program by deleting the C9 command.

It is a bit of a PIA, but I can manage and it looks like it will at least allow me to use the indexer.

Thank you all for the assistance.