The USPTO allows people to start using an invention publically, even selling it, before filing for a patent as much as a year later. Then also, they allow people to apply and say that they were the first to invent the thing in a patent owned by someone else.
It may well be that, following the original nullification of the LFN patents, Microsoft showed that they had invented and used privately (maybe for testing purposes) their long file name technology. Perhaps they showed proof that their invention was before the publication of Rock Ridge. Maybe there was some way that they could argue that the parallel development of Rock Ridge didn't render their method obvious to a person having ordinary skill in the art. But we'll never know because the hearing was private and so my (perhaps unreasonable) assumption is that the convicted monopolist cheated again.