When you have learned a signal, then loaded the Remote's contents back to ProntoEdit on your PC:

Go to button Properties for a button that has a learned signal.
It should display a blue bar looking like [C]Learned
Double click that, opening the Add_IR dialog.
Click the View IR button.

Select and copy (^C) the whole string of hex numbers that appears. If there is a scroll bar active, make sure you select the whole thing, not just what is initially visible.

Paste that into a reply here.

I hope it isn't too different in your version of ProntoEdit from the version I based the above instructions on.

I'm not even sure which version of ProntoEdit to try for an RC5000. I tried two versions, neither of which offer that choice.
So I don't know what RF options there are for the RC5000. If there are any, go to the RF tab of the device properties dialog and make sure "IR enabled" is selected.