Oh no, n900 built in Skype works like a charm for me. As well as Planet 3 and other 3 services.

The reason I wanted a Skype application supported by 3 is that they offer free Skype phone calls that are routed through their network. When you are on Three and call Skype it gets connected through their gateway rather than using 3G data connection.

Well, I have never gone over the limit with my unlimited 3 Internet when calling Skype from n900 but I found the call quality to be superior if it is connected through their Skype service rather than 3G - tested that on my Nokia E71.