I had the same problem with time i found out why
kits:
starters:
delay: 1760
items:
- 306 1 protection 1
- 307 1 protection
- 308 1 protection
- 309 1 protection 1
- 267 1 sharpness 1 fire
one of my kit layouts
with - 306 1 protection 1 on the item in the game it will give you the item with protection 4 + fire protection 4 on it
but with just protection in the game it will give you protection 4
why it does this im not to sure but that might fix your kit problems