The US banking system feels pretty backwards in terms of its reliance on checks where Europe has adopted electronic transfers. If the banks actually wanted to innovate here, they'd introduce a real electronic transfer system. The idea of scanning checks and sending around images (and presumably one day constructing virtual check images electronically and sending those) strikes me as remarkably backwards, but nonetheless a very clever solution to a real-world problem.
If you build a better mousetrap and try to sell it, but I decide to build my own copy of the mousetrap for my own use, wouldn't that be non-infringing?
It's not clear to me whether in this case the check scanning systems were in fact independently invented; there's certainly a hint in the article that meetings took place and the banks only implemented the idea once it has been disclosed to them ('willful infringement' results in triple damages, which could well explain the magnitude of the licensing amounts)