Well, with the upgrade to WordPress 2.6 and the changes in some of the plugins I was using I ran into a couple problems. The biggest is that Flutter, a admin panel change-eroo thingy (technical terms here) does not play well with WP-ecomerce. I am bummed to say the least. Seems like when they released the latest version of Flutter (formerly fresh-post) they forgot to make it work well. Anyway I assessed the probelem and decided it was not worth my time fixing it, enough people are complaining about a series of issues with Flutter and I expect a new version soon.
I had to decide though which plugin to keep and I chose e-commerce. I figure in the next month or so this will be easy to add back in. Interesting experience though.
If I have time I am gonna try to install the older version and see if that will work out.