After looking deeper into the issue I determined that the project had some kind of weird corruption:
- As I mentioned in the previous post only the .STEP version of the files added the PAUSE.
- The PAUSE was added only to specific 6 plates out of 11 (plates 4, 6 and 7).
- I added a new, 12th plate with the .STEP version that was on one of the 3 plate offending plate. There was no PAUSE added.
- Finally, I created a new, identical project and this time everything looks OK.
As I said… WEIRD!