The buttons aren't popping back up because you set them to Switch. The command buttons (Start, Pump Down, Store Data, Stop, Close All, Clear, and OFF) should be set to Latch on Release for their mechanical action. That would also eliminate the need for the Select functions. You should also probably move your device initialization and closing outside of the while loop. There is no need to reinit and close with each iteration. Also, use Index Array instead of changing your array into a cluster and using Unbundle.
I went ahead an made these changes to your VI. I also removed everything else that was being disabled.
I suspect you will need to add a wait between your Write and Read to give the device a change to react.
I had the buttons on latch before, but then they weren't working, so I used switch and then local variables. I changed that back.
I'm not sure what this did/why it worked, but I changed the Refnum to a control and then back to a constant, and now everything is communicating!
Thanks so much for your help everybody!