My personal theories on why DO students tend to perform better on COMLEX:
1) Faculty were open with us at my school that our exams were designed to prepare us for the COMLEX. Which, since that's what we need to graduate and become doctors, kind of makes sense. In the past USMLE wasn't as necessary, so designing a curriculum (heavier on the micro/pharm, easier on the biochem) and more for COMLEX and writing questions in an NBOME style made sense. The few faculty members I talked to about it did mention that they were starting to try to prepare us more for the USMLE as well, but, as in just about everything, change moves at snail's pace.
2) Additionally, I know quite a few of our faculty are COMLEX question writers, and I don't think any write for USMLE. Either consciously or subconsiously, this would make them write in-house questions more similar to COMLEX.
I doubt either of those things are unique to my school.
Edited: fixed a typo