When we parallel to the grid after 2 minutes or so the 100 A breakers drop out. We have only been outputting around 1 ~4 kW.

If we manually drop the breaker there seems to be almost no load change on the generator (so the 1~4 kW seems right), but our CT's are all measuring up around 90~100 A?

How is this possible? We tried our free excitation voltage at 237V and 243V to see if this would make a difference (on a 240 V phase-N) grid, with no change.

 

Are you sure the generator is in phase, and locked to stay in phase, with the grid?

And what else is on the load side of the breakers, besides that generator? Something is seriously amiss because 4kW in a 240 volt system ain't anywhere near 100 amps. More information is definitely needed.