I am pretty new to SEO (or at least new to being serious about it), so use my advice at your own risk.
My guess is that this stems from situations like this:
Powered by FORTUNE3 • shopping cart software or the other keyword perfect variations of it at the bottom of your customer's sites. Would they have put that there if you didn't pre-code it into the software and charge them money to remove it?
The sites are also all unrelated. You might think they are related because they are your customers, but is ray bans, jeep parts, car covers, and homeowners rights manuals, gun lasers, and all the other sites related to shopping cart software? None of them has any other mention of shopping cart software on their whole site, except for the forced link.
Also, these are effectively paid links, since you put them into the software by default, and you charge people $50 to remove them. Thinking in reverse (sort of), you are paying $50 to them to keep the link. It's a forced, or paid link.
Think of it this way, if you offered to your customers to remove it for free, or gave them a way to do it easily and told them how (even for non-techies, like a check box in the admin panel they use for processing orders), what percentage would remove it.
I used to have a store on Big Commerce. They did the same thing, except I could remove it in the accessible code, and it is one of the first things I did right away. I really did not want to be forced to advertise for them.
Anyway, I am curious to see how this plays out, as I suspect you are not the only shopping cart provider with this situation.
By the way, here is another example of it, and it is sure to catch them too. Go Daddy Spammy Link Building