I cannot find this setting since version 10 of DbVis was out. Because of that, as I may guess, using # as a "Single Line Identifier 2" for comments results in SQL errors.
It has moved to the Processing Controls drop-down menu in the SQL Commander toolbar:
That works. Perhaps, the explanation in the Tool Properties > SQL Commander > Comments needs to be updated to reflect this move.
Ah, thanks for pointing that out. We will fix it in the next maintenance release.