I'm seeing the same thing here. Adobe redesigned the TWCC for CS6, and this is not the first bug I've seen with it.
Premiere CS6 TWCC performs very very poorly in every way. It even earns the honor of performing worse than FCP7 TWCC. I really don't want to be rude to anyone but I'm pretty sure that people behind the CC effects in Premiere never ever touched video color correction in real life. I hope it will eventually get better thanks to Iridas / Speedgrade purchase.
In the meantime, if you can afford to spend an extra $300, Red Giant Colorista II works very well even if it get a bit buggy with DSLR footages.
I have had the same problem. Has anyone addressed this or found a workaround?