Not sure if this is related but I had a similar problem. It turns out I was using EAC to generate the wav files and I had the option to automatically generate m3u files turned on. It looked like MM was using the data from the m3u files rather the tags and would ignore changes to the tags that were ...

I'm currently using:

Windows Vista 64
Media Monkey 3.0.4.1185
dbPowerAmp CD Ripper R13.1
Exact Audio Copy V0.99 prebeta 4