maybe not relevant to your current problem, but eventually some helpful thoughts.
I spent some time in finding grounding issues :-) on different santorins (including our own). what I found out where to put attention to:
fischer panda is normally not isolated but there is an upgrade kit available by fischer panda (relais plus ready made cabling) that makes the fischer panda genset "amel-friendly". I installed it on KALI MERA and it works fine. without the kit you will have battery-minus connected to seawater when running the genset.
you should check the cabling at the shaft alternator, there is a strong possibility that the isolation of the cables break and a connection from ground to the housing occurs, causing a ground leak (battery connection to bonding system, positive or negative)
any changes in the alternator-system (new alternator or new shaft alternator, additional alternator...) can cause ground problems because most alternators are not isolated and therefore should not be used on an amel.
and if an SSB has been installed on a santorin that has not dedicated SSB grounding then this is also a typical thing to pay some attention to when looking for ground leaks (e.g. direct connection of grounding to the rudder...).
and (for sure not relevant to your actual problem but worth to mention): the original bonding - copper ground strap to the keel will break after about 10 -15 years, so should be checked also... :-)
SN120, KALI MERA, Trinidad