Post the pronto hex for a few of the signals you learned that don't work.

If there is something wrong with the Pronto Hex, we can probably generate clean copies.

In any case we would know whether the problem occurs in learning the signals or in transmitting them.

The most recent thread of "seems to learn OK, but nothing happens when sending" turned out to be that the learns were fine but the Pronto was set to use only RF for that device.

But there are quite a lot of these "seems to learn OK, but nothing happens when sending" threads and they have a variety of different answers. Looking at the Pronto hex that was learned is the best way to start focusing on what sort of answer fits.