Sounds like a bad ground or shielding in the start system wiring. Check what NG/N1 speed when the noise goes away during a battery start. Then see what relay, switch, etc is actuated within that speed range. Once you have an idea trace out the external power circuit and see if any of those items are affected by a EPU start. My guess is you lost a shield grd but you know how those gremlins are.... good luck!