If it is possible to put the wheel in the other way around, you can quickly verify that it is a frame issue vs. a wheel dish issue. (Your test with a different wheel clearly points to the frame as the culprit, but if this is possible, it would nail it.)
Cannondale purposefully does this, and you have to get wheels dished appropriately.
This would bother me, especially if you want to be able to run as fat a tire as possible, as this will be limiting.