Hi Squeaky
Hmmmm, so let me ask....how much were you riding, in weekly miles, before you started commuting? and how many are you riding now?
If you increase too fast then it is going to be a problem w/recovery.
The bottom line remains though, if your legs are tired, then your body hasn't recovered yet. If it doesn't recover then you can't get stronger. So when my legs are tired/sore/hurting, I don't ride (save for super easy spinning maybe).