The outcome is... the chorus IC was faulty. Replaced the IC and it is working perfectly now.
The D50 EPROM throws a start up routine where the CPU checks if the Gate array, Synth & dyna board INTs are present. Then the Gate array also checks if reverb and chorus are present. If they are all present the CPU boots up.
As the chorus was still sending I/O data the CPU (even if corrupted) the boot routine could not detect it's fault. And that made the whole diagnosis very tricky. I think there is no worse thing than an IC that only fails partially.