I just upgraded to Lion on my work computer and it seems like Spotlight doesn't index SMB volumes. This used to work for me perfectly under Snow Leopard. I've talked with Apple and they said it was never a supported feature, and just worked by coincidence on 10.6. Now it's not working at all. When I run the mdutil command in the terminal it says "indexing and searching disabled."
Can indexing be enabled for SMB data on Lion?
mddiagnose
and pour over the information. If it was removed, you might be out of luck, but perhaps you might uncover some hints or ideas. Sorry I don't have a better answer.