I have had a similar problem where at seemingly random times, the Rio remote just stops working. I normally have to power cycle the player and it comes back good.
I have a kenwood remote left over from another project which works with the empeg (probably a similar model to the original Kenwood remote shipped with the earlier models) and noticed then when the Rio remote stopped working the Kenwood continues to work.
Is there a reason for this?

Cheers,

Andy M