Ah yes, well it's just a matter of making sure exactly what's up. That's a weird issue and one I've not yet encountered or heard of.. you may be suspecting the right issue, that being the remote itself. I use the Sony that Clark has been selling for some time.

That mixer mode is the first thing I change, I really don't like how it works on a Clark.... full reverse all of a sudden during a turn? No thank you..

So all 3 of your boards will program except for those functions correct? Yea... suspecting the remote.