Programs Extended recently added an option to disable Alarm 1 Countermeasures itself. I'll need to check if I need to change something to be compatible with that.

the "POST-MID ALARMS" option didn't work for me on my recent campaign with Programs Extended's extended alarms. At the OMNI Foundry, on Alarm 1 Countermeasures triggered instead of Vigilance. I have a log file saved if needed. I wonder if PE's recent update caused a conflict in mod loading order where VP's logic for overwriting spawnGuards isn't being run as expected.