Here is the $64,000 question. As someone who may or may not work in the industry, I understand best practice is to not tell everybody and their mother that you have one. How are the holders of said TS (especially SCI) brandishing proof to the MSP? Most, if not all DoD entities are not going to give you a letter stating you have one. And if you are a federal contractor, your company's security officer shouldn't be providing that letter either.
Can I assume MSP is taking your word for it? I doubt it. You can provide a CAC for ID, but that doesn't denote a clearance.Certain installation badges you can only get with a clearance, but then, most of those are FOUO only.
I'd be interested to hear how that is being done, since I may or may not be in the pipe for this.
Bingo. MSP knows most agencies will not provide it. And therefore deny you because you can't provide proof.