I have the same problem as LilHobbes. Jim, I've deleted songs from the cloud and not then selected to update. Left it for about six hours, but when I then went to iTunes Match hoping for a library with 0 songs in, it is still telling me I have the 5000 that I had previously deleted.
Any other suggestions?
Turns out, I went back to my iMac and turned on iTunes Match again. Once I turned it back on, it did all the steps and had even more songs available on the cloud. I tried the 999 song delete and then did the update iTunes Match and the songs went down! So I'll continue to try and get it down to zero, but I guess going back to the original computer works!