I faced similar problems many times on racing cars where fans, pumps, etc. are feed from different voltage supplies.
The easiest way to cure the problem is to cut the diode's common trace on the PCB -not an elegant one, I admit.
If you want to keep the diode-protection however, you'll need to reroute this trace to a not switched +12V, like the flyback in ideal situations
I'd vote for omitting these diodes as good quality automotive relays (like all OEM BMW) always have a protection diode inside.