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Hi piemmeweb,
Random thoughts:
-Apart from caps going bad which you've covered
-State of the battery? It's not eating anything is it?
(you probably checked)
-PSU: It's old, knackered caps (etc) in this will give 'dirty' power possibly marginal voltages too - the kind of thing that tends to improve on warming...
...I hope not, but if your PSU has been mis-behaving it may have partly fried the chipset hence output on RTG card but none on AGA...
...I'd be tempted to strip the mobo down, hack in a new PSU & see what happens.
Oh, let's not forget cleaning socketed components & their contacts, making sure they're properly seated. (SIMS too - esp the ChipRam one)
All the best.
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