no idea on the flickering lights but how is the 480v secondary grounded?
it may not pass code but you can use some Y connected capacitors and ground the neutral point. you'll need 3 volt meters connected to an alarm so that when a ground fault occurs you will know it. resistors are also used for this type of situation, common on submarines and other mission critical systems where a single ground fault isn't a high enough priority to justify taking a system offline.