Upon teleporting into the fort, Neera keeps saying "Yes, I heard you! Now shut up, please." But when I tried to talk to her, it keeps saying, "You cannot initiate dialogue. Neera appears busy." Eventually, she just stands in the same spot, not far from Jegg facing the wall. From time to time, she disappears and only reappears if I warp out and then back in. Every time I try talking to her, I get the same message.

Has anyone else had this problem? Any ideas?

I remember having a similar issue to you, yeah. Unfortunately the only way I could get around it was by using the console to spawn in a brand new copy of Neera (which means she doesn't have her XP or items from the first game).

what mods did you install?