One possible reason that the OP might not get points is if the company negotiated a specific one-off rate for the stay. (e.g., A better rate than that property's standard "corporate rate".) I've spent about 2 1/2 years of my life in long-term Marriott properties and the points I earned was always specifically negotiated as part of the deal. I have done a fair amount of RI, a little SHS, and a lot of Execustay. In most cases, I got something flat - like 5000 points per invoice, where the rent was invoiced monthly at around $2k, give or take. Our company did a lot of business with Marriott in everything from catering at full-service Marriotts to a high-volume Execustay account, so the Marriott reps were willing to work with us a bit.

But the awarding of points in a lot of these long-stay scenarios is definitely not automatic. Once you cross 30 days (in many jurisdictions) you're getting out of the standard hotel business and into something more akin to an apartment rental, and the language in your lease is more binding than the terms of Marriott Rewards.

That said, the RI where you are leasing multi-month should at least hook you up with a couple points per dollar as a goodwill gesture - even if it's not being done that way in "the system". When I was doing my big volume with Marriott, I was ignorant of the elite statuses so I never even asked. 5000 posts on FT later, that seems pretty silly, doesn't it?