The native resolution of your plasma is more than likely 1024x768 rectangular pixels.
When you connect a PC to it, the EDID information given off by your plasma reports this to Windows, which then sets the resolution.
But you see why this is an issue. The inputs on the plasma can take in various resolutions (probably 480i/p, 720p, and 1080i/p) and adjust it appropriately to the panel. When Windows sets itself to the native resolution, it won't look as good because it's not being adjusted internally.
I would alternate between 1080p and 720p to determine which looks crisper/clearer, and stick with that.
Just make sure you only try resolutions that your plasma can handle.