It's hard to say what's happening without seeing your event sheet or debug output - are you using two separate array objects, one for each array file?
In C3 you can load multiple arrays from files in sequence as follows:
On start (or function, or whatever):
AJAX: Request array1.json tag "array1"
System: Wait for previous actions to complete
Array1: Load from JSON string AJAX.LastData
AJAX: Request array2.json tag "array2"
System: Wait for previous actions to complete
Array2: Load from JSON string AJAX.LastData