I'm not sure that naming the file M6.m1s will work.
First, make sure you have Mach3 configured correctly. In General Config, there are 3 different options for M6.
1) Ignore them.
2) Stop Spindle, Wait for Cycle Start
3) Auto Tool Change.
If you have it set to Ignore them, then you'll see what you're seeing.
As for the file name. Mach3 uses two M6 macros, named M6Start.m1s and M6End.M1s
When you choose "Stop Spindle, Wait for Cycle Start", Mach3 will first run M6Start, then it will wait for the user, and after pressing Cycle Start, Mach3 will run the M6End macro.
If you use the ATC option, Mach3 runs the M6Start only.