I'm not able to replicate the issue.
The PK1 format has byte 0x03 to indicate the Current Level when stored in the box, but I can't find any scenario where this will be set to zero.
Fixed in the latest commit
https://github.com/kwsch/PKHeX/commit/7ef5d9e547c46299f63da2282f58c670844a2a14
never-boxed pkm don't have this value set; PKHeX now handles the party->box setting of boxlevel