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If those measurements are correct then the back wheel may indeed be moving at a faster linear velocity. It might be losing grip and your traction control (if you had it) would need to kick in and reduce power to the rear wheel. The other option could be that the front wheel is in the air. 

Are those results with the wheels off the ground? As Fred said, if they're on the ground the calculated speed should be the same unless one of the wheels is losing traction. You don't really need to monitor the speed of both wheels anyway unless you're doing traction control, just pick one and use that for the speedometer like every other motorcycle does.

It really depends on how much power / torque you are talking about, and what kind of traction control system will be implemented.  If you aren't pushing the limits of traction in most conditions issuing equal torque commands to front and rear motors is probably going to work out just fine.  Where you get into trouble is when you are climbing a steep hill (which gives the rear wheel much better traction) and are turning a corner where you need the front wheel to set your course,  if you apply too much torque to the front wheel and it starts slipping just to maintain straight travel, you will have very little control to initiate a turn and could lose balance.  If you are just making a utilitarian vehicle where you want to get the best traction in all cases and maybe the front spins and looses traction sometimes, but isn't that big of deal because you are going slow enough that you just put your feet down to prevent a fall,  like the Ubco 2X2 , you can probably just give equal torque commands to the front and rear and hope for the best.

-ryan

Generally seems to have been implemented elsewhere as 30% front, 70% rear.
Your real problem is that you will lose half of the major traction advantage of 2WD if the motors are not actually physically geared together. With your design it will be possible to spin up the front and lose it, which is otherwise impossible with 1WD, and self-correcting with mechanically geared 2WD. In other words ... an advantage that can suddenly become a disadvantage.
Cas