I recently upgraded to WooCommerce v2.0.3, although I did have a few reservations because upgrading shopping carts always throw up unexpected problems.
Turns out, it did throw up some weird stuff -- now my entire site doesn't use WooCommerce's default CSS even though I have it enabled. Previously in v1.6.6, everything displayed fine.
I understand its a custom theme, but is there anything that might have conflicted with the inclusion of a WooCommerce CSS Style?
It works fine in TwentyTwelve, though.