This might possibly be a case of Improve linking between groups assigned to entries and JabRef's internal group system · Issue #8836 · JabRef/jabref · GitHub . It’s been a while since I personally have looked into this issue, but it seems to be related to listener issues. Please check, if opening/adding a different library and switching between the two will update something the groups in the GUI. Maybe, restarting JabRef after the import/opening might be a fix? Please repost your findings.
Also, what version of JabRef are you using right now? You can find this information under `Help > About JabRef`