JohnSFine is probably going to correct me.
It is my feeling that these signals are not clean.
Several things can cause this.
1. Weak batteries in the OEM remote (or possibly the learning remote.)
2. User error.
3. A protocol that DecodeIR.dll is not set up to handle.
3. Something wrong with the programming of DecodeIR.dll
4. Wrong version of something, or something is not in the correct spot.
Let us start at the bottom of the list and go up.
4. Make sure you have the latest versions of all the tools. Also, make sure that the up-to-date version of DecodeIR.dll is in the same directory as IR.exe
3. JohnSFine is only human. I say this because we have not invented Robots like Data from StarTrek:theNextGeneration (yet). So he must be human. Humans can make mistakes. I think the odds of JohnSFine making a mistake are 6,258.7:1, approximately.
2. User error. It happens to the best of us. You have learned other remotes as you have created other upgrades, so this might be less likely than if you were, say, me, about a month ago. But you might want to dim the lights, turn off other sources of IR, point the remotes head to head 2 inches apart on a flat table, and you might want to wait until you see the flashing lights before you press the OEM button, and you might want to keep pressing it until you get the two flashes that say it was recorded. Also, you are not holding down the learning remote button the whole time are you? I didn't think so.
1. Weak batteries. Go out and buy some nice new batteries. I hear they might sell you some at radio shack if you ask nice.
It is at this point that JohnSFine will correct me and report that your signals are very clean and that the problem is in some way my fault.

So let me apologize in advance!
Good Luck,