I think that one explanation is that P&F aren't pressing a claim to own the trademark; they're claiming nobody owns the trademark, because it was legally abandoned due to being out of use during that gap period.
If they had pressed an abandonment claim back then, I think they would have had a strong case, but I'm not sure how the passage of time, Stardock's purchase of whatever rights Atari had, and subsequent development of the game may have impacted the strength of their legal arguments.
I've done my own non-professional analysis of this mess at http://forum.uqm.stack.nl/index.php?topic=7015.msg76832#msg76832. The short version is that Paul R.'s contract with Accolade seems to give him a lot more control over the SC1&2 copyrights and distribution than most developers today have. Stardock did not seem to be aware of this when they purchased Atari's assets, and PR appears to have avoided setting the record straight about what he felt he owned up until the recent counterclaim.
Note the careful wording in PR's emails:
"I've talked with Fred and I am afraid at this time we aren't interested in the Star Control assets you purchased from Atari."
Stardock interpreted his lack of objection during this email thread as tacit acknowledgement of their claims. But PR never actually conceded that he agreed that Atari owned the copyright and distribution rights Stardock believed it paid for. It seems more like PR knew that his contract had returned those rights to him, but he chose, for whatever reason, not to correct Stardock's apparent misunderstanding.
So, at this point, my (non-lawyer) opinion is that Paul R. has the stronger legal case, certainly over everything but the trademark, and the trademark itself is shaky due to possible abandonment. However, I think Paul R. also bears responsibility for most of the drama, because he was not more forthcoming about exactly what he felt his rights were. Had he communicated more clearly - ideally before Stardock paid Atari in the first place - this could have been resolved more amicably.
As things stand now, I still hope that Paul and Brad can get together, with good lawyers, and hash out a settlement that keeps this out of litigation, and lets everyone get back to making the games we want to buy.