Inconsistent shifting issues after changing wheel
There are many variables that you should look at when switching rear wheels, and wear is not really the first place to look, nor is the tire type.
The first area is the hub - are the hubs the same? I am going to assume that both wheels have the same number of cogs on the cassette (which eliminates the 8/9/10/11 speed differences), or you would be having other problems. Hubs can have slight positional changes, millimeters, for the freewheel, depending on the manufacturer, so the cassette will seat in a slightly different location on each wheel, relative to the centerline.
The second is the cassette. SRAM and Shimano cassettes have slightly different spacing, Shimano and Campagnolo have much larger differences in spacing - you want to stick with the same brand cassette for maximum compatibility. Also, road cassettes and mountain cassettes have narrower and wider ranges of gears, respectively...if you have a 12-32 on the mountain cassette and a 11-23 on the road cassette, you will have a load of extra chain when running the road wheels, and that can cause shifting problems.
When switching between wheelsets, at a minimum, you will need to make slight adjustments to the rear derailleur...or you will need to swap chains (or remove a section of the chain, which you can do easily with quick connects), it more than likely will not be a seamless transition.