My guess is that the two seperate ground rods need to be tied together. If the FIM's have a common ground, then all of the grounds are tied back to the other system via the conduit. As such, you may need to tie the two isolated system ground rods back to the main house ground or go to isolated ground outlets.
As it is right now, you have the potential for multiple levels of ground within your system. Besides each ground rod that you have going, each circuit can have slightly varying levels of conductivity to ground. This is due to differences in resistance, especially if you have multiple connections along the way. If you used straight runs of wire without tying in anywhere else ( that is what a dedicated circuit is ), this should not be a problem though.
I would also take steps to weather-proof / seal the ground rod connections once you've got everything straightened out. No matter how good of a connection was made, moisture, dew and corrosion will find a way to get in there and gradually diminish all of the effort that you've put forth. Sean
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