Sorry, let me try to clarify. Your assessment isn't correct, but that's because I might not have been clear.
Think of it this way. Flirc is a language translator. Each computer is listening to flirc. Both flircs can say 'space bar'. Each computer can understand and respond to this when flirc says 'spacebar' However, they don't both always respond at the same time.
You can then teach one flirc to learn spanish, and one flirc to learn french. They will both translate and repeat the word 'spacebar' when they hear it in their corresponding language that they understand.
If you take your remote, and say the instruction in french, one flirc will say spacebar to the computer connected, but the other one wont, because it only speaks spanish.
Now take the languages we identified as spanish and french. When logitech speaks spanish / french, it's actually speaking a unique infrared protocol. There are thousands, and they don't conflict. That's how you can control multiple devices in the same room, with a single remote. The remote is speaking each unique language that only the specific device understands.
So now you've added the profile: Flirc, NVIDIA to your harmony. All flircs understand the NVIDIA profile.
On the one you don't want to respond to that, go to File->Adavnced, and disable the built in NVIDIA profile.
Add another 'language', or protocol to your harmony for that second flirc that the first one doesn't understand. Choose an ambiguous device that doesn't exist in your living room. Like a panasonic TV. After adding it to your harmony, rename it to, Gaming PC, or Movie Machine, or whatever it is it's connected too. Then pair that new profile with this flirc. You can pair any signal that remote sends out with spacebar, and the other one wont also send that to the machine, because you never paired that protocol.
Let me know if that's a little more clear.