Ryan,
It is possible that you are calling into another DLL (e.g. an instrument driver) that was linked against the instrument driver runtime (instrsup.dll). While cvirte.dll is a superset of instrsup.dll, if a program links against a particular library, then that is the library it needs to load. It can't somehow know that it can use cvirte.dll instead. That is why your app is loading both.
As far as correcting the distribution problem, all you have to do is make sure to select the Instrument Driver Run-Time subcomponent of LabWindows/CVI Run-Time Engine in addition to the Standard Run-Time item.
Mert A.
National Instruments