Bad remote (less likely since you say TV controls work). Bad sensor on STB. The other common problems are interference with the IR, which you say you addressed such as line of sight from remote to STB sensor. Various TV's, both PLASMA and LCD/LED, do often interfere, and there are a few other devices reported to interfere.
Try another remote, you can ask for a free one if you don't have one handy. Next thing after that is report the box as bad and get a replacement.