Hello, try something simple like coolant on/off first,(M08/M09) just in case it's a safety interlock preventing auto use (door open, low air pressure, low hydraulic/low slide oil/ low spindle oil etc stopping the spindle from running).
Otherwise does it work ok if you write a program in auto mode and run it?
Some machines are picky about the order of code too, for example you may have to issue the S code then the M code (S1000 M03, but it should run ok if on the same block)
Hope you have some good luck, Cheers.
PS: How's the weather this time of year ?