Hi again, Larry.
I've just had a listen to the 'bad' wma and it's definitely the midi track that's creating the conflict in sound. It's out of tune with the backing.
Jazzmandan solved your problem for you. You needed to set your Windows system to 44.1 kHz (which you did). Doing this won't affect the files that have already been created by rendering but, when you render a new file (after altering this setting), it will have an effect. That explains why you were successful when you re-rendered.
What version of Windows do you have?
Below is how I have my system set-up (Vista 32 bit).
1. Right click on the speaker icon in the System Tray.

2. Select "Playback Devices". Then click on "Speakers" and select "Properties".

3. When you enter into the "Properties" settings, select the "Advanced" tab.

4. Activate the option that says "Allow applications to take exclusive control of this device" (#3 in the above image). This will ensure that BIAB will always operate the soundcard at 44.1 kHz even if another program comes along a resets it to 48 kHz.
Regards,
Noel