You didn't specify your fare class but could it be the 50% for deep discounted fares that actually give you 100% when you book through CO.com?

For example...

Discount Economy Class Q, I, S, W, T, X, L is 100% if booked through Co.com, otherwise 50%.

If they do indeed drop off as you say, CO should honor it. I have never seen less than 100% EQM on any of the ONEPASS code flights I've taken.