OK, well, for what it's worth - should anyone ever have this problem, and don't quote me on this...
When buying a USB IR transmitter/receiver they're all generally for IR devices such as phones, PDAs etc - and are mainly used for data transfer (files).
I believe (but don't claim to know) that these USB IRs use the mid-high range of IR frequencies. And remote controls use low range IR frequencies (and er thus why the remote controls wouldn't communicate with the USB IR)...
I could be talking nonsense as I'm just equating all the comments and crapola from various forums and websites.
But eventually, in order for me to use a remote control with my PC - I had to purchase a cheap MCE remote control, just because it came with a USB IR specifically for remote controls, or for low range frequencies (I'm assuming this as it comes with the remote control).
So now I can use my preferred remote (Philips Prestigo) to control my PC!
This was just in case someone who knows nothing about this type of thing should stumble across this....
Good luck all.