JXDP1 is a CPU Jtag Debugger header (Was used for Factory Tests to check the CPU Socket worked)
JGPIO1 is a Header that was used at the factory to Program the Chips on the Board
JSPI1 is the BIOS Factory Programming Header to directly Flash the BIOS onto the Bios Chip before it gets Packaged
all 3 you asked are all Headers MSI put on the board for internal Programming of the components and to run tests on the Motherboard to make sure it worked
There is also one pin header that has no label near the vga port. The speaker is connected there.
I would like to find out if my MSI board MS-S115 has LPC_CLKOUT0 or LPC_CLKOUT1 pin?
This board has soldered Atom C2000 cpu (C2358) which has a bug (AVR54)
There are possibilities to workaround that bug and get the system running again "c2000 100ohm resistor fix"
I try to find out if I can apply this fix also on my board ms-s115