One possible cause could be accidentally creating an alias for the /set command.
If you have a line beginning with /set somewhere in your alt+D aliases file, that makes it intercept the /set command and perform that alias instead.
To see if that has happened, paste this into any editbox:
//echo -a $isalias(set) $isalias(set).fname
If it says $true, then that's where the alias is located. If it says $false, then that's not the problem.
If the /set command works when it's inside a script, but not when typed in the editbox, another possibility could be an ON INPUT event which doesn't correctly handle editbox commands beginning with the forward slash.