My series II has never had this problem. I ALWAYS write my program with M998 at the end of the tool path.
Example:
Start code
T1
M6 (tool discription)
S WHATEVER M3
G0 XY (where ever you want to start)
G43H1Z1.
M8
G4P2. (give coolant time to come on before cutting)
G0Z.1
G1 ( start tool path )
TOOLPATH
G0Z1.
M5
M9
M998
M0
CHANGE TOOL
CONTINUE
M998 WILL NOT work unless you first reference the machine. If you don't reference the machine, It's like the machine has alzheimers disease. It doesn't know where it is.
I have never had a problem if I use this procedure.
You can buy GOOD PARTS or you can buy CHEAP PARTS, but you can't buy GOOD CHEAP PARTS.