Tell us what control system you're using. This might not sound important, but it tells us what the software can do.

What device did you use to learn the commands?
Can you give us the Pronto Hex of the commands that aren't working right?

Also, is there anything consistent about how the commands don't work right? Do they sometimes work and sometimes not work? How many times in a row? Always work the first time of the day? Never work the first time of the day? Work in some particular way after you wait, say, ten minutes?

I'm just trying to flesh out its behavior in case it's not as simple as it could be.