There were two military contracts in the model of 1899 revolvers. The Navy contract serial numbers are 5001 - 6000, and the Army contract serial numbers are 13001 - 14000. Furthermore, 38 caliber 1899's were first caliber roll-marked at about serial number 7400 or so; your gun is too early to be caliber roll-marked.
Both of these military contracts were chambered for 38 long Colt, which does not fully seat a 38 special. If, by chance, the serial number on the back of the cylinder is within one of the two ranges mentioned above, then that might explain why it does not seat a 38 special cartridge. It's remotely possible that the cylinder on your gun is an over-run from one of the two military contracts, and again would not seat a 38 special cartridge.
If, for some reason, the cylinder on your gun has been replaced, (even if the serial number on the cylinder does match the butt number) it may be chambered for 38 long Colt, and not 38 Special.
Mike Priwer