If I were you I would use some of the available Frameworks out there, that handle Platform independence.
I wrote a 3D-Game as a hobby project with a friend of mine, the server being in Java and the clients running on Windows and Linux. We ended up using Ogre as 3D-Engine and OpenAL as Sound-Engine, both platform independent and available under LGPL.
The only things I really had to write separately were the whole Socket-handling, reading the config from file system and the initialization of the System. Compared to the rest of the Program, that was almost nothing.
The most time consuming will be to set up the entire project to compile under Windows and Linux (or Mac), especially if you're concentrating on one and only occasionally check the other for problems. If you have one in your team who checks regularly for these problems while they're being produced you won't have that much overhead from that as well.
All in all compared to the programming of the game itself, adapting it to different platforms is almost no effort, if all frameworks used are well written, platform independent systems.