Don't you just hate rejection? It makes you feel so... rejected. Well, you can mope around, kick the furniture, and fling obscenities at the faceless producer who wrote the damned letter, or you can forget about it and start writing another script. That's the only way to do it, otherwise you'll go into the backyard and start digging your own grave.
Can you believe the niceties that may flicker within the letter? Who knows? Should you believe the reason for rejection? Who knows? I sure as hell don't. Don't agonize over the letter; don't pick it apart trying to decipher it. It'll never happen.
People don't get a kick out of hurting other people (at least I hope not). No one is going to tell you that your script stinks, but neither is a producer going to falsely praise your script.
So... how do you know the real reason for rejection? You don't and you won't. Just accept it as fact and move on. It isn't the end of the world. Everyone gets rejected -- even established writers. The difference between the professional and the novice is the way in which rejection is met. Professional writers do not take rejection personally, nor do they let rejection question their ability to write. They take it as they see it. The company is not interested in the script for whatever reason.
Maybe the company really does have something similar in development. Maybe their "slate is full" -- for real. However, if the letter talks about the script in-depth, or the producer calls you personally to reject the script, you have reason to smile and pat yourself on the back. Okay, so the script was a no-go, but the producer thought enough of the script, and your ability, to take the time to call you or write a letter of praise. You can't take the letter to the bank, but you've just walked the first few steps.