I am sorry for wasting your time. I figured out what I was doing wrong.

I realize this is not an issue with the True PVE plugin. However, I figured I would put this out there in case anyone else had a similar issue. I am also notifying the developer of the other plugin this morning as well. So about a week ago I updated all of the event plugins on my server (Sat Dish Event, Junkyard Event, etc, as well as Convoy and Armored Train). It appears that there is something within the Convoy plugin that is causing the rules set forth in the True PVE plugin to not work properly. For the better part of 3 days (I work full-time and go to college full-time, on top of dealing with Crohn's disease) the players on my PVE servers were unable to kill ALL NPC in the game. The regular scientists, the heavy scientists, underwater dwellers, tunnel dwellers, and all of the event NPC's were completely invulnerable. I could sit 2 inches from their face and unload an entire clip of an M249 into their face and they would not die. I thought maybe my True PVE cfg might have been out of date, so I told the plugin to start with a brand new CFG and added a few flags and removed a couple of rules, and all was good on the server. However, after 3 hours I went back and every NPC was invulnerable again. I soon realized this coincided with the start of the Convoy plugin event. So I have removed the Convoy plugin for the last 3 days and everything has worked as should be expected. So this made me believe it was some odd interaction between the most recent Convoy update and the True PVE plugin that was causing the NPC's to be invulnerable on my server.

I was being stupid and did not pay attention to the Convoy plugin being updated again the same day to fix this issue. So do not be like me and ensure your plugins are up to date and you pay attention to the notes for plugin updates.