I decided to post it here since I am going to tell stuff that could be considered spoilers.

I walked into the Van Graff Energy Store in Freeside. Normally, your first entrance triggers a small thing where Gloria is talking to a guy about him trying to weasel out of paying full price. To test the weapon, she vaporizes one of her own thugs. However, my game is hanging on when she gives the order. The guy just stands there.

He isn't holding a weapon at first. When she orders it, he equips one and stands there.

Any fix for this?

Are you using any mods which add custom ammo types? While working on a mod of my own I found that trying to add a new ammo type to a weapon's list will make the game consider it the 'default' ammo for that weapon, and since Jean-Baptiste isn't carrying any of the new ammo he won't fire.