I use the rate a lot - and have sometimes had to ask for points.
The argument is simple. The rate is NOT 50% discount for each night but a full qualifying rate night followed by a free night. This means that the first night is eligible and the second night (irrelevant for point earning in IC's) is ineligible. If this argument is resisted don't get into a discussion simply asked for your request to be escalated.
This does appear to be one of the problems. Some 2for1 rates show on the folio at 50% per night rather than as full rate first night, zero rate for the second. Others are clearly stated on the booking confirmation as 50% each night. The latter trigger the rejection, the former get points.
I have advocated for years now that PC bookings should clearly confirm one will earn points for a stay, or not. This should appear on the rate selection screen as well as the final confirmation one. Either that or all rates bookable on its website should qualify. This is the on really serious problem with this program which has yet to be satisfactorily resolved.