I have found that my speeds are the same when riding with a MTB or with a Road Bike along the same route. Unless one day is particularly windy. I think it has a lot to do with rider position in my case, or perhaps overall geometry. I lay across the bars on my mountain bikes and on my flat-bar road bike, whereas with my other road bikes I always use the drop bars.
I have found that I am faster with my 15 year old road bike with flat-bars (when laying across the bars) than I am with my supped up road bike using the drop bars. This probably has a lot to do with the wheels as well, the old bike has Mavic CXP 30's and older dura-ace hubs, the new bike has Fulcrum racing zeros with cult hubs (the older CXP's are more aero, although quite a bit heavier). BUT: Here's the kicker. I've got an old Cannondale Jekyll with fat tires and a monster of a rear rim (Mavic D321), and my speeds on this bike are only slightly slower than my speeds with the other, more aero bikes! I am basing the speeds off of GPS tracking via cell phone.
I am wondering if this is more to do with the bike geometry and fit, or overall aerodynamics?
I travel 21km twice per day to work and back for a total of 42km per day. My average speed with the heavy mountain bike is about 26-28km/h whereas with the road bikes it is usually between 27-30km/h.