Compare & Merge works differently when automated vs manual

I'm comparing my ER Studio DA physical model with a live SQL Server 2017 database.  Our models contain ONLY tables.  Most but not all contain foreign key relationships.

I save my setup in a .cmo file and run compare using the GO button on page 1.  I then run the same compare with a macro.  There are no options when running via macro, everything must be set in the .cmo file, so code can't be an issue.

The results between the two methods however are not the same.  Specifically, when run via automation, the results contain extra tables to be merged.  The tables already exist and so when merge occurs the operation duplicates the tables in the model.   I've examined the characteristics of the tables that get duplicated but can find nothing similar between them.  They seem completely random with the exception that rerunning the report or merge selects the same tables.

  • I've pretty much proven this can't be something I'm doing wrong.  It's now reported as a bug. 
    Any attempt to automate model updates from a live db with this tool is DANGEROUS.  It can ruin your model. 

    Don't even try until this is resolved!  

    I'm pretty sure it's not related to the DB I'm using so I'll take that out of the title and drop the tag.