First of all, thanks a bunch for picking up the game! I really appreciate it and am honored you wanna pursue all the endings.
It's my policy not to give away the exacts of how to get an ending publicly, but I can give you some hints. The True Ending can be achieved by being careful what you use and say in the bunker-- some items you can keep, and some things must be done in a specific order. Or, there's a hidden way to cheat it in... uh-oh!
With Beracus dying, you'll also need a specific item (something... dangerous) and Lee needs to be in a state where he wouldn't care if Beracus lives or dies. This is a tougher one to get, as it's more specific, but again, you could secretly cheat it in, if you know how!
As for the endings glitch: I've heard of one other person with this problem and I'm truly not sure how it could be happening. The endings only have ONE place where they are triggered to go off, and so you should HAVE to get to that place in the script for the game for it to work.
Do you mind letting me know: If you're playing the Itchio version of the game? If so, is it for PC, Mac or Linux? Or are you on the Steam version of the game? Have you ever had any version of the game prior? (The update before this for example, or a beta test file?) This will help me in fixing the problem.
Thanks so so much!