Any spring rate difference with the hub stands should be minimal not affect crosses. It might affect ride heights, but even then it would be tiny and easy to predict. It should also be pretty straight forward to get the same center of pressure under the hub by modifying the hub stands. But I suspect that this isn't necessary.
Any effect the hub stands had on one corner, they would have the same effect on the opposite side. Thus they would not change crosses.
Just a guess, but I think you're making Jims and my point about tire inconsistencies. Did you try rotating the tires on the same car or swapping them from the other car? I've done that and it always changes the crosses. Even brand new radial tires will be off enough to see it in the crosses if you swap them around.
What did you use to provide slip at the scale/hub stand? Not having the flexible rubber tire will magnify any binding issues, so you need something to release binding at all four corners. Old tricks like trash bags won't work. You will need something like a ball bearing turn plate at all four corners.
I'm sure your saw what you saw. The question is just why.
Just a data point, most, if not all, F1, Indy, DP, Grand Am GT teams use hub stands.
Here is a picture of the Brumos guys using their hub stands. It looks like that might be inset to get the COP closer and they do have bearings at the bottom to release bind. http://www.racemsm.c...achment_id=1844 Click on the picture for a larger version.
-Kyle