When you said "It didn't work", what was the circumstance of it not working? You didn't run chkdsk in a dos box, did you? It doesn't work that way. It has to be recovery console, or windows error checking tool. Was it reported that it found no errors, or that it found errors and they were fixed?
Also, since you have a 40GB drive, your MFT may very well be filled up if you have many small files. For example, I once installed Forgotten Battles and Ace expansion on a 20GB drive. When I tried to install Pacific Fighters, it reported a full drive, although I had 8GB left. It occured to me that FB, Ace, and PF all are made up of tens of thousands of small files, and my indexes were maxed out. This could very well be the case, as unlikely as it sounds...