There was some nonsense talk about Cthulhu Tech having issues which turned out to be only hearsay - and Shadowrun's troubles are in the process of being ironed out. (It was a writer's copyright issue that's being resolved.)
So far I only know that BT's chief layout gent has left, but everything else I've heard can't be confirmed.
Either way I wouldn't worry about CGL being able to pay for the licensing fees. SR and BT is their bread & butter. They've done financially well enough to expand their table top games not once, but twice (CTech and Leviathans) - if anything the outright loss of $850,000 dollars is what's troublesome. (And I'm guessing CGL's recent foray into finding a new hardcopy publisher is what brought the discrepancies to light. I got ten quid on it.)
For the record, GW is the largest table top game producer in the world with an estimated worth of around $300 Million USD. (I should know. I worked for GW US Corp in late 2007, early 2008.) But not envy them - they're lucky to still be around.