The following code causes both elements from id 0 to be set to -, even though I want only one to be set to -1. Am I just creating a re
Yes. Both valueArray and labelArray reference the same underlying array. To make a copy, use slice():
valueArray = labelArray.slice(0);
NOTE: Slice() only copies 1 level deep, which works fine for primitive arrays. If the array contains complex objects, use something like jQuery's clone(), credit @Jonathan.
valueArray is just a reference to labelArray.
What you want to do is clone the array. You can do this using jQuery.clone() or a similar cloning function.
Am I just creating a reference to the labelArray […] ?
Yes, exactly. valueArray and labelArray still identify the same object, which hasn't been copied.