Some items from Quark show quark.jei.hint.preamble at the start of the hit text as show

Also, when a hint is added via kubejs, the text is appended onto the previous hint instead of making a new entry

Mods in use:
Quark-4.0-462
Zeta-1.0-30
jei-1.20.1-forge-15.20.0.106
emi-1.1.21+1.20.1+forge
kubejs-forge-2001.6.5-build.16

I can't reproduce your second issue. For a temporary fix to your first issue, add the following as an entry in your assets/quark/lang/en_us.json

{
    "quark.jei.hint.preamble": "[Quark]\n"
}

Looks like quark references this as quark.jei.hint_preamble (with underscore) and EMI's info is trying to grab quark.jei.hint.preamble (with period). Good luck and hope this helps!!!11!!