First of all, I'm not an expert in running databases under wine, just a few general hints: Please update to the latest wine version, if you haven't already. Run your app from command line and post the output. Did you follow the instructions from http://wiki.winehq.org/NativeOdbc ? Maybe you need to declare DSNs for sql2008. Which odbc driver are you using for sql server 2000, and how did you install it in wine?
