ZZap,
Welcome to the world of ungrounded systems!
Possible reasons why the ground fault alarm comes in and out: the fault is resistive, and the threshold is on the margin for the monitoring relay; the fault is related to local ambient conditions, such as rain, steam, sun if you are lucky enough to see it this time of year, etc.
What are loads on the system? If they are, say, field-mounted instruments on switchgear or transformers, this kind of fault is not uncommon.
There are some interesting instruments which can detect and locate ground faults. The one we use is called a 'Grouser' (not 'growler', which is a toy that the motor repair guys use). The instrument works by injecting a fairly small low frequency AC current into the loop formed by the faulted pole of the DC system and the earth. A sensitive detector using a coil on a ferrite core traces the injected current along the core to the location of the fault. It can be a laborious process, especially if the fault is at an awkward location such as the top of a power transformer.
Prior to buying the Grouser, we constructed a similar arrangement using a signal generator, power amplifier, and a coupling transformer. The arrangement worked well until the day when someone cranked up the 600W power amp somewhat while tracing a high-resistance fault, and knocked out part of the 11kV network by operating one of the protection relays. Ooops! Moral: be careful if the loads are critical.
This link shows the instrument, about halfway down the page. I can't find the manufacturer's website at present.
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If we learn from our mistakes,
I'm getting a great education!