I noticed that also, a while back. I read a post about a month ago that Stardock was going to fix that.
I have paid with PayPal a few times at in the StarDock store and since I have a some extra cash in PayPal, I thought I'd use some of it to pick up Z71s's new windowblind the other day. I was unable to find a choice to use PayPal at all.
It's not that big of a deal since I can use a credit card instead, I was just curious why it was not an option.