I am not at all sure as I have very little experience with DOS shell, but I suspect that you might be running into this clause of phase 2:
If the parenthesis counter is 0 and the parser is looking for a command, then ) functions similar to a REM statement as long as it is immediately followed by a token delimiter, special character, newline, or end-of-file
The ( would not have incremented the parenthesis count because it was not looking for a command token at that point; I hypothesize that at the point of the ) that it was looking for a command. I might be misreading the intention of the description.
Anyhow, if my suspicions are correct, then you should replace the ) with ^)