I use Harmony, IgorPlugUSB-IR-receiver and Eventghost-Software. I also used Girder before. Both config work.
Harmony emulates other remotes pretty well. Your problem should be in pc-config, not in harmony. Can you control PC with other (not universal) remotes?

BTW, I created my harmony's HTPC-device from scratch (as a device of type "TV-Video-Combination" from unknown brand) and learned it with commands from another universal remote (it was a pocket pc with remote control software). This allows me to add new commands if I need them. I also use the second remote to check if PC can detect new commands, before I push them to harmony.