I have a guess at what causes that. If you post pronto hex for any of the digits, I will know whether my guess is correct.

Some IR protocols have what is called a "toggle bit". With that, there are two different versions of each signal.

The original remote alternates versions with every keypress. The device is programmed to reject a signal if it is the same command and same version as the last command accepted.

If that is the problem, there are a variety of possible work arounds. For example:

On some remotes, you can program a panel switch on every keypress (in addition to sending the signal) so you can have two identical looking panels containing opposite versions of the digit signals, so as you press each digit, it sends one version and switches to the panel that would send the other version. A regular Pronto doesn't do that panel switch well enough to be a good solution to the toggle bit problem. But I don't know about an iPronto.

There are other possible solutions, but I'd need to see specific Pronto Hex to give specific advice.