My Mac keeps teeling me there is no more room on my Start Up Disk

This is the message I get: there is no more room for Applications on your Startup Disk. Eventually my iMac freezes. This cannot be true as there is most 90% of a TB of room on my hard drive, same with my external hard drive (another 1 TB of mostly unused space). This seems to be a new problem that has occured since my computer was restored with OS 10.8.2 after the original hard drive failed. Any ideas how this can be made to go away, permanently? It caused me to need 9 restore attempts prior to successfully restoring from Carbonite.