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ie net start mysql
if mysql is installed. Same with some exchange programs and Microsoft Sql. In the db side, it usually means a log file was deleted. Also found problems with net.exe related to the latest sp2 for XP, but nothing for Win2k.
But to not be able to just type net.exe is wierd.
Maybe someone else with a bit more knowledge can help you. There are some viruses that will rewrite the net.exe file, but if I remember correctly, the net.exe is wrapped in a bunch of gui stuff for windows and if it was not running properly, you should be seeing other problems as well.