It sounds like you have learned a dirty command. You may have to clear the screen that it is on, or you may have to clear the entire remote. If the screen reset and full reset don't work, try the one at the bottom of this link.
[Link: remotecentral.com]When you relearn the command, load it again before you do any other programming, and test it out. If you still have problems, try either a short burst or a long burst from the original remote.
Sometimes adding a command that doesn't do anything might help. This is done by pressing the button of the command you want to learn, and the button that doesn't do anything, in quick succession before the 3100 beeps.