The whole problem was in apparent short between one of the fan module components and a corner of hard drive cradle. The most interesting is that it happened a couple of hours after the player was inserted in a dock. Initially at the installation I didn't have access to hard drives with cradle to test the proper clearance and adjust the components appropriately.
I had to replace bbq'd fan components and now everything is back at full swing.

You are right about one thing - it takes a lot to "smoke" empeg.

The intermittent initial misbehavior of empeg after memory board installation was probably due to the fact that I booted it many times with serial connection without ever attaching hard drives.

The actual measured current draw of fan controller with fan rotating was 0.05 A

I am running fan, lights, stacked memory and digital board in my main unit for a year now without a hitch.