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I stay in IHG hotels a fair amount booked through work's travel agent - indeed I'm about to check in to one when the train gets in. Always get the points and credited stay.

Don't get them if you book it through booking.com or similar though (although hotels.com at least used to give you a 10% cashback as a credit for free nights, which is handy when you can't stay in one chain)

Booking through something like Concur is different. Concur doesn’t charge the hotel a fee for booking through them. Concur gets paid by the company.

I bet Concur gets paid for having slow page loads and thereby discouraging employee travel. It's the only explanation.

I’ve had mixed success asking to add my loyalty number at check-in, even if I already provided it to the aggregator.

RIU hotels does. If you are part of their program after you stay you can go to your profile and add points for previous stays that weren't booked through them

source: staying now in the hotel and done it ;)