First off, removing the batteries doesn't automatically reset the remote as the programming is written to non-volatile memory. To reset the remote use the "Clear All" function which is found in the "Configure" section.
Anyway, have you found device codes for the components that your programming? If so, it might be a better idea to program the missing buttons using advanced codes instead of learning, that way you can program them to any button you like, not just the learning buttons.
Check out my web site for more info on this remote.
Rob.,
http://www.hifi-remote.com/