Right, I have checked my customs forms. When I landed, they put a very specific 'Document Number' in the middle box at the top of each page, and stamped each page of the listing with a CBSA date stamp in the box in the bottom right hand corner of each page of the form.
If you don't have these, you should.
Perhaps the second CBSA guy was confused when you showed him the official form YOU completed, thinking this is what they had done. Point out to him that it does NOT have an official document number added in the box next to the 'Name of importer', nor has it been date stamped in the 'CBSA Stamp' box at the bottom right, and stress that YOU completed the form in advance thinking this is what you had to do.
Just FYI, my document number was 4312B4-17-069 (yours would of course be different, but this just give you an idea of the format).
HTH