Via @JakieJake9725 on Discord:
With several mods active that add items to the hotbar (in this case, Calamity, Joost's Mod, and AlchemistNPC), there isn't enough room to add kRPG's items, and so some items (typically the spell glyphs) end up not being generated.
This is probably an issue with adding items to newly generated players in general - tModLoader may just increment a counter representing the inventory slot it's on and doesn't do any kind of error checking to add items directly to the inventory instead of running off the edge of the hotbar.