Most likely, you are experiencing a firmware issue. Samsung has had repeated issues with IR codes sets varying from one version of firmware to the next. Most likely, the newest HLTs support the HDMI3 code, while earlier versions do not. Same issue with the first runs of DLPs(HLM) supporting discrete power, but not input, then from version 314 and up supporting power/input, then later still supporting discrete color and aspect.
Even if your purchase was recent, it doesn't mean that you have the latest version of firmware. The set could have been stored for quite some time and need to be updated by Samsung to the latest firmware to support the HDMI3 code.

I don't have a HLT in front of me to test, so this is purely speculation based on experience.

Jason