Uhuh LD; come across this little number before. Finished up with splinters from scratching my head too much!
The gen-set must be earthed, and so too an independent earth provided for the installation. Any earth between the genny and the installation can be removed if you get nuisance-tripping provided that the main earth terminal is securely grounded. I have even seen the PME link removed in standby mode - but this shouldn't be required.
The RCD will be downstream of the change-over switch, and nuisance-tripping will also occur from on-load switching transients causing an imbalance in the active-neutral, combined with parallel paths through earthing arrangements. The intermittent nature may be due to this only occuring when certain loads are 'online' at the time the change-over occurs.
If the genset and installation are electrically seperate ( from the earthing point of view ) you should have no problem as the ECL exists only 'within' the installation 'circle'.
