We've been seeing this on our older 6th gen HP desktops with 120GB drives. We've discovered that our SCCM instance is reserving a big chunk of the drive space as its cache - we've had to reduce the cache size used on the devices down to around 5Gb otherwise the drive just fills up and no one can logon.
We've also ordered a bunch of 250 GB drives so thats my half term job to replace those in around 60 machines and rebuild them.