So although the object name is FREArray, the way you initialize it in Java determines if Actionscript expects a Vector or an Array.
Initialization of Array:
FREArray.newArray(int numElements);
Initialization of Vector:
FREArray.newArray(String classname, int numElements, boolean fixed);
It says very clearly in the documentation:
http://help.adobe.com/en_US/air/extensions/WS982b6f491d178e6d6565d9b1132a79a012f-7ff8.html
I just overlooked the fact that the constructor doesn't create either, its specific. Thank you for your help in this issue. I have upvoted your comments.