Our Official Check Vendor is telling us that we can put a stop payment on these "official checks" at any time (do not have to wait the 90 days).

These "Official Checks" are not drawn on our bank and are not shown on our general ledger.

Is this information true?

I would refer your vendor to your state's version of the Uniform Commercial Code. Assuming they use the model verbiage, the if your "Official Checks" are drawn on a bank other than yourself, they would meet the definition of "Teller's Check" which still has the same 90 day period before a claim of a lost/stolen instrument can be enforced.

UCC 3-312

"Teller's check" means a draft drawn by a bank (i) on another bank, or (ii) payable at or through a bank.