Hi Jesse,
I opened up your project on my computer and I was not able to reproduce this error. I saved the project file again after modifying it and returning it to its original settings.
Open up this project in your computer and see if you are still seeing the problem.
You mentioned that you installed LabVIEW on different computers and the same problem persist. Did you try to copy the code from the included VIs over to a brand new VI and make a brand new project? Is there a specific VI which causes the settings to not save when you include it? Query Database by Cert Number.vi is missing for me, and that's the only subVI that I can't load up. See if removing that from your VI makes a difference.
Please let me know what you find out. Thanks!
Yi Y.
Applications Engineer
National Instruments
http://www.ni.com/support