Thanks for helping me people.
Ok, I'm going to need to cheat my way through anchorage without mods, excluding PN and TTW, to see exactly where this has occurred. I have unsuccessfully tried the code completequest xx0009bf after you talk to montgomery the first time, but it doesn't work. Have quest ID's been changed by TTW or perhaps i'm doing the cheat wrong?
Oddly, loading an Anchorage save with only TTW and PN, I can actually see the grenade icon, in the simulation. That's not what we said happened during the sim so that's weird. Completing the sim, the icon is gone again.