First, rule out the car itself by having everything installed but the empeg pulled out of the sled. Get the car engine running and see if the scanner works acceptably in the dash. If it doesn't work, then it's got nothing to do with the empeg, it's the car or the wiring.
(Note, I'm assuming you've got a way to listen to the scanner without the Empeg being in the loop, right? If not, jerry-rig something...)
Then rule out the tuner module by de-installing it completely.
Next, rule out ground loops by disconnecting the RCA cables of various components and seeing if the problem clears up when you do.
Then set the empeg's timeout value to 5 seconds, and set it up so that you can pull its ignition sense wire. With the car running and the scanner listening, pull the ignition sense wire connection to the empeg. The empeg should drop to standby mode. After 5 seconds, it should drop out of standby mode and fully power down.
This will allow you to see the difference between the "empeg on standby" and the "empeg fully off" modes.
If the scanner gets better when the empeg goes into standby, then you've got some kind of crosstalk in your wiring. For instance, maybe your scanner antenna runs along next to your amplifier power cable.
If the scanner gets better when the empeg goes into full power-off mode, then it's RF interference from the empeg's CPU, electronics, and/or hard disks. Note that the empeg passes FCC regulations for a car stereo, so it's "within spec" and there's nothing that can be done about it. However you could work around it by leaving the empeg's timeout really short and figuring out a way to shut it off when you use the scanner.
Maybe it's something as simple as changing the order of the items in the dash (put the OTHER unit on top instead of the bottom). Perhaps that would be enough to change the RF fields in the dash so that it works acceptably.
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Tony Fabris