Even with their MIT-derived designs, battery manufacturer A123 has also been having problems. They seem to be tied to the fortunes of the Fisker Karma:

Since Fisker Automotive rolled the Karma, a four-door luxury plug-in hybrid sedan with a price tag of $103,000, off of the production line in December, the California-based company has been plagued with problems. At the end of December, Fisker issued a recall because of a battery pack coolant leak that could have caused the Karma to short-circuit. A few weeks later, Fisker issued another recall for the sedan because of a software problem. A few months later, in February, Fisker announced that it is renegotiating some terms of the Department of Energy (DOE) agreement for the $336 million balance on its $529 million loan. A month later, the Karma died during a Consumer Reports test. Later in March, Fisker announced that it will replace the batteries in the Karma after the manufacturer A123 admitted there is a glitch.

Captain Hybrid says battery development is just very hard:

In contrast, battery makers are constantly searching for new materials, combining them, testing them, and then waiting for the results. It's a physical sciences challenge. And it's limited by nature. "You're always working with something new, like a cobalt oxide one day and a manganese oxide the next," Brodd said. "You can do anything you want to those materials, but you aren't ever going to get any more energy out of them than the thermodynamics allow." That's the main reason we're still searching for the ultimate EV battery 100 years after the New York Times declared that the technology had arrived. It's a painstaking process. Battery makers know this, but with venture capital at stake, they often project their capabilities in ways that are part fact, part hope. If they don't, funding may not follow as rapidly. The result is that hopes are raised and then dashed, as they have been over the past few months.