I had a lot of sleep/wake issues when I built my HTPC towards the end of last year. I found there were a few steps that needed to be taken to get it all to work as expected. In no specific order....
1 - Make sure USB port continues to receive power in the low power state chosen. (May need to check jumpers on the motherboard.)
2 - Make sure the device, and anything in the chain of execution is allowed to wake the pc. (Device Manager. Not only the IR receiver, but the USB controller as well.)
3 - Make sure the remote sends the correct command and it is interpreted correctly by the IR receiver. (Check the timings on the harmony remote, some commands may be too close together and are interpreted incorrectly by the pc.)
4 - Depending on your video card, you may or may not need to change specific low power states for the video card. (MST was good for this step.)
Best of luck. I know this stuff can be frustrating.