Control Reference created by scripting removed in build

I have a template VI that is duplicated with another set of VIs. Within, there is a control that is copied, replaced on the VI panel, and, using scripting, a reference to this control is placed on the BD and wired to a subVI. It works and produces a new VI with no broken arrows. 

When I build this VI into a packed project library, the references are removed and the resulting VI is broken.

Creating and wiring this reference manually does not exhibit this problem. 

This problems exists in LV 2014-7

Is there some reason why a reference created using VI scripting would not be preserved in a build?