Here's a few things to try:
1) Open up Pokemon/Save/options.dat - Open this file up using Notepad. Look at the Volume| tag. If it says Volume|0 then you have your problem. If save data isn't removed upon uninstall, then that would be why it was left alone to persist when you reinstalled. Set this value from anything between 0 (no sound) and 100 (max sound).
If that fails then try: (2) Back to the Windows Desktop. Right-click your sound icon in task bar on bottom right. Click the bold text Open Volume Mixer. Scroll right past the Device bit and through Applications, look for Pokemon 3D in the list. Is it muted? Is the sound low?
Finally, if that fails, then: (3) This one is a longshot and more of a last resort stab in the dark. Open up Pokemon/Content/Songs - try and run a WMA file to see if it will play. I did say that this is a longshot but if sounds work but not music, maybe your windows is having trouble with WMA file types.
Hope this helps.