Hmm, this is a tricky.
The flashing is related to patch save, however it's Function - that should do this, not Function +. There's nothing in the code at all to make the LED flash with the Function + button!
There's something clearly wrong in the area of these 2 switches, although it's hard to tell what off the top of my head. You may need a multimeter / continuity tester to work this out.
Function - (SW2) is connected to D13 on the Arduino
Function + (SW3) is connected to D12 on the Arduino
Can you test these connections with a multimeter (i.e. push the button and see if the connection is made).
Also, is there are short between D12 and D13 on the header?
Let me know if you need me to go into more detail about this.