The problem is that BART isn't bringing in enough money to help the extension and so there's not enough money to run the sucker. Since it was supposed to be a dual operation, both sides want the other side to make up the difference. In some ways, this is your Bay Area transit in a nutshell-- a bunch of agencies fighting amongst themselves for an ever-decreasing slice of the pie.
What's happening this time around is that both BART and Samtrans proposed budgets in June. According to BART's budget, Samtrans is going to pitch in 11.2 million. But according to Samtrans, they're only going to pitch in for only $5 million. Even us non-math types can figure out that's a difference of about 6.2 million.
So what are they doing now? Talking, talking and more talking. Even talking about how to avoid such snafus in the future. Good thinking.
All things considering, we just don't imagine these negotiations would be that easy. That's a lot of money to be fought over. On the other hand, it's much better than having Samtrans send Guido the Killer Pimp out to settle things with BART.