One thing that I would LOVE to see is a way to make remote antennas go up only when the radio is active, not anytime the empeg is on.

This is already built-in to version 2.0 of the software and with the antenna extension cable. The antenna extension cable (assuming it's correctly wired and is not affected by this defect) contains a separate antenna-remote-activation wire that will only turn on when the radio is on.

If you are using the main sled's blue "Amp Remote" wire to raise your antenna, then that's your problem, the antenna is up when your amplifier is on. Re-wire using the tuner extension cable correctly, and you will have the thing you desire.
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Tony Fabris