I wouldn't worry too much about the colour of the cap. You mention a short but don't have anything to confirm that. A simple multimeter across the cap will confirm a short if it's there but I doubt it. It doesn't look like a bypass cap - even if it was shorted, I doubt the whole empeg would stop working.

The clicking is probably the hard drives trying to move heads or spin up. Are you sure your power pack is OK? I'm not sure the self-healing fuse will necessarily click.

CH