Programs disappear from Add/Remove

I have an interesting problem with Program entries disappearing from my Add/Remove programs dialog box. This has happened at least three times. It doesn’t appear to have any rhyme or reason to it. I’ve taken off downloaded programs (WEB) and installed programs and it seems to be random. When I remove a program, every entry on the list vanishes. The software still functions, but it is not listed on Add/Remove. I the only way to remove the software is with its Uninstall option. Anyone have any idea? I’m running Win98SE, the MS site doesn’t seem to helpful about this.