Illustrator Package function issue

I've had an issue recently when using the package function in Illustrator CC. I have a document that contains linked files, with some links used more than once in the same file. When I use the package function, I select "copy links" and "relink linked files to document" and have it save everything to a new final folder. When I go to the newly packaged folder, it is creating duplicates of the same linked file for as many times as it is placed in the document with a number after it. For example, if I'm using TREE.psd two times in a document, it's packaging it as TREE_1.psd and TREE_2.psd. I've only recently started having this issue, and it's a real problem when I have files with multiple links used multiple times. I had one document go from 25 linked files to 100 and had to delete all the duplicates and relink everything in the document. Does anyone know how to solve this? I don't know if this is as simple as an option that I need to turn off, but I haven't been able to find anything. Thanks!