And, the magic 8-Ball says....
Oh, there are other pieces of gear out there. And you went and hit the Abort button ( don't do that!) So, you probably have some external device that is initialize on First Call? being True. Look for the First Call? Primitive, a Globally initialized Feedback Node or an Uninitialized Shift Register in any external device init routines and ENSURE that all devices receive a device clear, DC, EVERY time you start your top level vi. You may have left a device in a state like "armed: waiting for trigger" that needs to be reset wirh DC, before the device can respond to anything else.
Yup, I think that old 8-Ball is still in good shape
"Should be" isn't "Is" -Jay