I installed the MarketPress plugin ( http://premium.wpmudev.org/project/e-commerce ) and found that it broke all my portfolio links. I couldn't see any relevant settings in either the plugin or the theme that I could tweak to fix it.
I finally found the solution was to update my permalinks. I didn't have to change them, just re-save them. It was already set to use postname so I just clicked on the Custom Structure option with "/%postname%/" in the input, clicked save. The end result is that the permalink ends up still being "postname" and it fixed the portfolio links.