Ah damn this doesn't sound good =/ From what you've said, it is the power transformer. The big round thing that looks like a big ball of coils with all the wires coming off it.
In all honesty, i haven't owned it very long but when I bought it, the guy I got it from said "it's never let him down" and "it's been a real work horse" so i took his word for it. When i have it plugged in, i've been playing my bass through it but I usually run the EQ totally flat with a tiny (and i mean tiny) boost in the high end. I have the pre amps on the 3500 set so the Tube pre is at 12 o clock and the Solid State is as 9 o clock just to blend some of it in so in no means am i pushing the amp.
I'll see if i have any other small amps laying around that i can connect the line out and effects out to one of them to test it all. As it's currently 2am, i obviously can't do that until the morning but i'll give it a go once i wake up. In the 10 minutes it actually stays on for, the amp sounds great. The rear fan spins but blows out extremely hot air. I will check for the smaller fan on the inside that you're saying about though.
Typically, i brought the amp from a guy in Bristol but live no where near there. The good news is that Hartke/Korg UK is only about 20 minutes away from where i live so I might drop it in to them some time soon.
Thanks for your help so far though, any other advise would be appreciated!