Each airline chooses how many miles to give credit for on various tickets. CO has chosen to only give credit for the smaller number of EQMs for the less expensive tickets on most partners (and on CO flights if you don't buy them at co.com). CO makes the rules for their program, and this is one that they have repeatedly said that they are very happy with the effects of. It may not seem fair to you, but this one isn't likely to change any time soon.

And for what it is worth, all the alliances have similar arrangements on the super discount fares. Some carriers don't even give credit in their own program for some fares they offer.

Caveat Flyor.