It took me THREE tries before NARA would even answer my inquiry regarding my dad's discharge papers, even though I HAD filled out the appropriate request forms properly.
After my third attempt about 5 years ago, they sent a letter saying that they were destroyed in the fire of 1973. That may well be, but as you stated there are times when they give this as the standard answer for any requests.
I personally know of people who have been fed this line, but who later find out that the docs were available because through other means eventually received them. Sometimes it's because they knew someone in higher places etc., who knew how to get things done. What a shame.
One researcher told me that it was basically due to lazy employees who couldn't be bothered looking into things. If you got one of them, then things didn't get done. If you got the right person, then voila!
Sorry you've had to go through this bull. The line about how your dad should have kept his original serial number, well excuse my French but how the hell should HE have known that. He went down to the draft board, volunteered and they did the rest. Like HE'S supposed to know. Good grief! 
Proud Daughter of Walter (Monday) Poniedzialek
540th Engineer Combat Regiment, 2833rd Bn, H&S Co, 4th Platoon
There's "No Bridge Too Far"