I'm the cause of this confusion, so I should clarify. What I was half-remembering was not in the Help file at all, it was a dictum of Leo's at the very end of this thread in the Forum:
To quote: "You can't mix DOS batch flow control and Opus commands as any Opus command causes the batch to be split in two.
You can either run the Opus commands via dopusrt.exe /acmd or use the equivalent DOS command instead, e.g. del."
Mixing DOS commands and DOpus commands seems to muck up the order and flow of the commands when "Function" is set to "MS-DOS" and the batch file contains "If" or "Goto" commands. I haven't pinned down the situation any more precisely than that, and I could be completely off the track.