Yeah, this happens sometimes. I was recommended to disconnect the Zune and close the software, then wait a few minutes and replug them in, and then the Zune will sort itself out. Of course, this sometimes takes awhile, took me almost about 10 hours before my Zune realizes I have 1Gb left in space.
Or you can just erase all content or format the drive with a certain button pressing on the Zune.