Ok, this is really weird. Yes it is. And I never set that. But what is really strange is it is grayed out and I cannot figure out why or how to unselect it.
-------------------------------------
Ok, sorted it out. If you accidentally select "Top level application window" and then customize it, you will get the the "Show front panel when loaded" checked and grayed out. If you instead select "Dialog" or "Default" first and then customize, you will get the "Show front panel when loaded" unchecked but still grayed out. Seems like there is no option that lets you control this manually. That could be a bug. I don't recall this being always grayed out in the past.
As for the 66 VI that always want to be saved, that looks like an unrelated problem with this project.