Jeff,
Your theory of same muscles being sore would hold true in the gym, where exercises and motions are repetitive, and all conditions and variables are controlled. On the track though, it's a much different story. There is no way, even under the same conditions, you are going to do 2 laps back to back exactly the same.
You mentioned your speed was off this weekend. Perhaps it was from riding too tight? Not being loose and relaxed woudl definitely call different muscles into play. Maybe one weekend you have a near fall and have to dab with your foot to prevent crashing. This could strain muscles and cause soreness. Perhaps one weekend you are more coinceous about gripping with your knees, and the next weekend you are not.
There are way too many variables that come into play to try to compare muscle soreness from weekend to weekend. Events during the week will also play a role, as will hydration levels and weekly nutrition.
J&K