Its going to be tough to work on that 8.6 style version ini API (There was a major overhaul of that palatte in 2009 and the versions never played well together)
That being said: making changes to vi lib is probably going to cause more trouble. I would suspect someone accidentally corrupted the vilib on the PXI and would see if their is a known good backup around before going further.
Looking at you code picture. I would strongly recommend getting that reference on a Shift register instead of tunnels into and out of the auto-indexing for loop. you'll have some strange things happen to you if Key Array is empty. Which, may actually be the cause of the original problem since the reference won't close and the file won't write in that case! With an empty array the for loop will execute zero times and the rereernce out tunnel will have a default value "Not a refnum" a SR fixes that.