That's the standard behavior for IR protocols that include a "toggle bit".

There are two different versions of each command. When you give the same command twice in a row, the device requires that you alternate between the two versions.

Post a couple samples of the Pronto Hex here for help with a protocol specific solution.

For some toggle-bit protocols the Pronto has special support built in, so you can replace the regular learned signal with a special form that makes the Pronto do the alternation.

For other devices, it is best to find a "do nothing" command and then edit all the learned signals, so they each send the correct command followed immediately by the "do nothing" command. When you press the same command again the device doesn't see it as twice in a row, because of the "do nothing" in between, so the device doesn't require the alternate version.

There are at least two other basic approaches to solving the problem that may be appropriate in more difficult cases.