I'm pretty sure your signal is NEC1 protocol, but at 40Khz modulation instead of the usual frequency.
That's exactly what this signal says
900A 0068 0000 0001 40BF 0EF1
The problem is that the Pronto ignores the higher frequency when the signal is recognised and converted to 900A format.
If you get a worse learn, then it doesn't get recognised and doesn't get converted and thus it works. But then the repeat was wrong.
You "fixed" that by making the whole signal repeat. That is not duplicating what the original remote would send for a long press. Instead you are duplicating what the original might send for many short keypresses done very fast. Depending on which key you do that to, the behavior difference in the actual device (for many short presses vs. one long) might be trivial or might be serious.
The trick here is to generate a correct enough Pronto Hex string in 0000 format that it will send the right thing, but incorrect enough that it won't be recognised and converted to 900A format by ProntoEdit.
I did exactly that in a few recent threads with exactly the same (40Khz NEC1) issue, but I forget the details at the moment.
Edit: Found it. Try this for the power code (the one that was command 0EF1 in 900A format): 0000 0068 0024 0002 0168 00B4 0016 0016 0016 0016 0016 0016 0016 0016 0016 0016 0016 0016 0016 0043 0016 0016 0016 0043 0016 0043 0016 0043 0016 0043 0016 0043 0016 0043 0016 0016 0016 0043 0016 0016 0016 0043 0016 0043 0016 0043 0016 0016 0016 0016 0016 0016 0016 0016 0016 0043 0016 0016 0016 0016 0016 0016 0016 0043 0016 0043 0016 0043 0016 0043 0016 06D9 0168 005A 0016 0F47 0168 005A 0016 0F47
To produce those with MakeHex, I used a .irp file consisting of this:
