Scientific-Atlanta's cable boxes have been notorious for being sensitive to IR overload, but it's usually only an issue when using IR emitters with gain set too high. If all your other devices are working fine AND the box operates fine with the factory remote, try rebooting the box and see what happens. Another thing you can try is setting the repeat for all associated IR codes from "3" to a lower number in the MX Editor software.

If all else fails, try sticking a piece of electrical tape over the IR receiver area (it's located on the lower left of the box's display window).