I think it's a multitude of factors:
1. Standardized test-taking ability. I think this may be a factor in some cases. There are many non-trads like myself in DO school, and our test-taking ability isn't as finely honed as some of you young-uns. Stem? What's that? lol.
2. Math skills. IMO, the real difference between MD's and DO's is our math skills. Most DO students I've talked to (myself included) suck at math. The reason our MCATs "suck" is largely due to low scores in physical sciences, which is largely math based. When I took the MCAT, I hadn't taken a math course in 15+ years. Is it any surprise that I scored 10's in Bio and VR, but an 8 in physics, despite strong A's in both Physics and Chemistry in Undergrad?
3. Poor research-related skills. I hate research. I have never honed these skills and I don't care. I went to med school to be a community doc, not be locked into academia. That being said, there are more than a few "research-related" questions on the USMLE. Types of studies, epidemiology, etc. We are NOT taught this in school (at least, not at my school), and you can be pretty much assured that DO students regularly miss these questions on the USMLE.
4. COMLEX was too easy. This happens to all standardized exams from time to time. This is why they are adjusted every few years. This year (lucky me) COMLEX has "raised the bar". This means you now need to get more questions correct to get the same score as previous years. There will be more failures this year (~600...it used to be ~400/yr) than in previous years. This occurs every few years in USMLE-land too. I think a new USMLE change is coming next year, if I recall correctly.
5. Different material, harder/easier questions, etc. Hard to tell. The rumor is that the COMLEX questions are more straight forward. First or 2nd order. USMLE questions, judging by the ones I've been doing on USMLE-world are 3rd order or greater. So, maybe the USMLE questions are "harder". Who knows. I think this argument is the weakest of the bunch, as it's very personal. I, for example, suck at Micro and Pharm. If I get some 3rd order micro questions, I will find the test very hard. Give me some phys and path and it'll be a piece of cake, no matter what the order is.
I also don't buy the argument that DO students are "dumber" or "not as good students" or whatever. I will buy the fact that we are a different population, with different goals, and different skills. I, myself, am a non-trad with a wife and an 8yo daughter. I would love to be a gunner and get straight A's, but I can't do that and maintain a stable family life. So, I live with my B's and like it. DO school has been a much better fit for us than almost any MD school could ever have been, largely due to locations (MD schools tend to be in not-so-family-friendly areas) and the PBL curriculum at LECOM-B (which allows me more flexibility in time management than most lecture based curriculums found at most MD schools). So, I don't care that we do "worse" on the USMLE, as a group. I feel prepared, and that's enough for me.