Latest version (210401) is flagging one of my Colosseum starters (Espeon) as illegal with "Invalid: Unable to match an encounter from origin game". I got them using PokeFinder.
I don't know why, but Espeon's PID is being read as coming from a different seed, when it should be the same. You can check that they're seven frames apart as it should inside the seed being read from Umbreon.
If you make a PID to IV search in PokeFinder, they show at different seeds. Espeon is showing the same as PKHeX, but Umbreon is different.
If I search the seed C591894E with the IVs I used for Umbreon, the same PIDs are 7 frames apart as they should again (this seed is never shown in PKHeX):
I don't remember this happening with previous version of PKHeX but I can't find it anywhere. Here are the mons:
196 - ESPEON - 36C8B67CC615.ck3 197 - UMBREON - B11A222B1D5F.ck3