Anytime you alter a vanilla script it for some reason does not get packed automatically. You have to then manually pack the .pex and .psc respectively. I opted to just ignore doing that and duplicate, rename/save-as or even just create new ones in order for the CK to properly detect and automatically pack the .bsa for my mod. I always re-pack when I update my mod as a safety precaution so having to manually add new items would get annoying.
Sadly it means I had to make my mod a complete overhaul. Which it was in spirit anyway but I didn't like being forced because of a silly bug in the CK.
EDIT: Yeah I had lots of complaints on how my mod wasn't working for others but was for me. Really pissed me off.