You can't load the contents of a 4.x PC card onto 3.x. They aren't the same (note the different files edb, xtr). If you want to create cards for loading onto the spyrus, you need to download the vcenter(s) to 3.x poll book and create them there.
Just to get you ahead of the curve a little, Mike Brown reported to me that once he went through this exercise, he couldn't actually get the 3.x smart cards to work with the 4.x ballot station. Same cards did work with 3.x ballot station, so it looks like there is a problem with the compatibility stuff on 4.x ballot station. He's been on the road, but said he'd submit the bugtrack once he got back. You might as well confirm the finding (and submit it yourself if you want), but I thought I'd give you a heads up since you'll likely see the same thing.