If you still need to program the remote to the Samsung, slide the mode switch over to TV. Hold mute and select for 5 seconds, and the TV light should blink twice. The following codes are listed to work with a Samsung:
10060, 10812, 10702, 10178, 10030, 11959, 11903, 11575, 11395, 11312, 11249, 11060, 10814, 10766, 10618, 10482, 10427, 10408, 10329, 10056, 10037, 10032, 10019, and 10264.
As far as the menu button not working... I'd suggest trying another remote, if you have it, just to see if it is an issue with the receiver detecting the command from the remote, or the remote having an issue with transmitting the command to the receiver. If you can get into the receiver's menu with the IRD's buttons, and you have an RF remote, you can try to program it to RF to see if it may just be an IR issue.