Nethunter became semi-broken

Well I don't know how this happened, only thing I can say is that I did the following (nexus 5):

Flashed Paranoid Android (it's now heavily tweaked but I don't think it affected any system files)
Flashed Kali Nethunter on top of PA
Flashed GApps

At first everything was working fine but now everything seems to be broken except the kali terminal. I can still start programs like reaver, aircrack-ng, msfconsole, wifite etc from it but if I press on launch wifite button in the launcher I just get a standard terminal with the following:

su -c bootkali wifite
Unknown id: wifite

Or when I want to update chroot

su -c bootkali update
Unknow id: update

Services don't seem to be working either? Does anyone know what to do? Do I really have to flash everything again or is there some fix available? Thanks for your help!

I've tried reflashing nethunter and keeping PA and it didn't fix my issue. Is is an issue with PA?

Try flashing supersu. PA's built in root isn't compatible.

Did you recieve this errors when reflashing the new version of nethunter over your current Rom?

Everything is working fine for me with no troubles,

Everything is working fine on stock.

@photonicgeek
Do I simply have to install it from the play store or do I use the nexus root kit to re-root PA?

Whatever you want. It all installs the same thing. I recommend the app though.