Once the file has been deleted from the projects folder and all media from that project has been deleted it should disappear. Are you sure there isn’t some rogue media from your project still floating around?
Try selecting all drives, one of the projects that is supposed to be gone, then have it show everything–master clips, media files, precomputes. If something pops up delete it. If nothing pops up try a program like MDV or MediaSift (both free), or Media Mover (not free but you can download a fully functioning demo for 30 days). Links to them can be found here:
https://forums.creativecow.net/cgi-bin/new_read_post.cgi?forumid=45&postid=861257
They should help find any media that Media Tool may be missing. Otherwise, I’m not sure how to get rid of projects from the Media Tool menu. Usually it means there’s some media from them left–now whether Media Tool can find it is another matter, but between Media Tool and one of the other programs above you should be able to find everything.
Best of luck. Let us know if it works.
Mike.