I've run into, or rather created, a new issue.
My current setup has the antenna power (power to the amp for the in-glass antenna) comming from the factory head unit. So, in order to listen to the EMPEG radio I need to turn on the stock radio. No biggie, but I thought it'd be a more elegant solution to have the empeg power the antenna amp.
So, I moved the power lead from the factory HU to the antenna lead on the tuner and when I did that the empeg refused to boot. It behaved as if there was no power.
So I disconected the factory HU. Then the EMPEG started working and the antenna amp got power but the system made a loud pop when it shut down.
Anyway, I'm back to powering the antenna from the factory HU. I haven't spent any more time troubleshooting, it's too damn cold in the garage to spend more than an hour out there anyway. My current theory is that it's a groudning issue of some kind.