I have v1.08 beta (for the headshots), and I tested this with that version and didn't have this problem.
I made three levels of a simple room with 2 Colonels w/shotguns and 3 health packs.
I let them take my health from 500 to 400 then when I went to the next level I picked up all the healths and it went back to 500.
I'll try this now by setting the player health to 100 like you did and see if it happens.
Brb
Okay, I set player health to 100 and I went to level 2 with 60 health just as you did.
Then , I got shot some more then killed the colonels and was down to like 43 or something.
When I picked up the health is went back to 100.
I think this is just because you are using an old version.
What version of FPSC are you using?
Nevermind that question, I see now that you are new, so you probably have not even installed any updates. (you need to)
If you upgrade, you may want to try
version 1.07, because 1.08 is still in beta and people have reported a missing wall bug.
So, until that is fixed, v1.08 might hold up your progress if you plan to release your game sometime soon.
Good Luck, and welcome to the forums.