The new remote should work fine with both units, provided you have recent software on them (and you said you did).

I don't know why this would be happening to you, it doesn't make sense. Can you literally place them side by side and one will respond while the other one won't? And you're sure the Kenwood remote still works on the old unit?

Or is it just that the remote itself is working intermittently? Maybe a low battery or loose battery contacts?