See this thread for some info:

http://talk.maemo.org/showthread.php?t=52046

When you are on the VPN the original N900 browser works if you install another program called vpncgui. Apparently the settings get reconfigured for the MicroB browser, but most other applications on your phone will not by default know the route through the VPN connection and will not work by default. This applies for things like Skype and the Application Manager. I do know know a solution for this problem.

Hopefully someone can help.