Have you seen
Phillips RC5 infrared remote protocol page
**broken link removed**
You need to understand how data is transmitted then you can understand how it is decoded.
If I get it right you input device feeds a signal of this type to the PC serial port. There the plugin converts it to the hex equiv.
The two ways to decode such a signal come to mind.
The first is to sample at 1/4 and 3/4 bit. HiLo is a zero LoHi is a one.
The other way is to measure how long each Hi or Lo section is. You can then write code to translate that to bits and then to your hex digits.
Both of the above have to deal with the start sequences. Note the toggle bit, the same key does not send the same signal every time.
But I do not think you need to go there yet. There is a good chance that you are sending the wrong codes or the right codes at the wrong rate.
If you can get your hands on a RC5 remote you could compare its output to yours using the scope. There are some x-in-one and other universal remotes out there that can stand in for most remotes. Handy to have when doing this sort of thing.
I was having a bit of trouble following you post, HTH.