Asman - You're definitely correct that the copper's interrrupt request is getting overwritten. I tested this by commenting out the manual call to the interrupt routine in the startup as follows:
move.l cop_int_vect.w,cop_int_address
move.l #.interrupt_code,cop_int_vect.w
; move.w #%1000000000010000,intreq(a5)
Then when I ran the routine I got no colours written by the blitter routine that runs in the interrupt at all proving that the interrupt never gets called by the copper...
I'll keep looking to try and resolve it.
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