Hey Sailor Steve and Jimbuna, thanks so much
JScones, thank you for putting us right, your explanation explains much.
So flag4, therefore AlacrityPC does NOT disable SH3CTSR.exe, because SH3CTSR.exe only goes into memory AFTER AlacrityPC has finished closing everything else, after which SH3CTSR.exe then loads SH3. So any settings you change in SH3 Commander will be loaded together with SH3, ie they are not affected by Alacrity PC which then also sits in memory awaiting your command to restart everything which it will do when you press "X" as already discussed, note: restarting AlacrityPC wil have no effect on SH3CTSR.exe, so you don't need to worry about SH3CTSR.exe exiting before SH3 Commander has rolled back, no matter when you press "X".