How about too many ports? Maximum port density for a 6509 is 384 ports. Try pulling some of the boards and see if it starts to work correctly. These are "classic" boards so they should work in any slot.
Do a show module when you unplug one power supply. If it shows power-deny then your power supplies are too small to individually take care of the switch. You may not be set up to be redundant in this case, instead of say two 4000w powers supplies tha...
Could you maybe find a disaster recovery firm to clean out your switches? Maybe they have a solution they can soak the boards in to clean them off. There should be someone out there, think about all the companies that have fires, water damage, ceilin...
VLANS and Layer3 switching aren't interchangeable. Wouldn't you need to actually segment out your network to use Layer3 switching(actually routing)? VLANS are still a Layer2 technology ... right?
I had this when I was setting them up to be redundant and upgrading the IOS at the same time. So I would guess either your redundancy is setup wrong or the IOS versions do not match. Pull the working one, upgrade and config number one, then put numbe...