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I just upgraded to version 6 from version 5. I'm probably missing something obvious here.
The first time I used it it downloaded headers for my subscribed groups no problem. But now when I try to update headers for a group it doesn't show any new posts for the last day and a half. I don't have any filters set as far as I know, and it's connected to the server because I can download from the groups old headers.

You see them download? What happens if you reload the group?

I tried reloading the group and still no luck.

Sounds like they're not getting saved then. Did you import headers from 5.59 or is this a fresh group? If it's not a huge group, I'd purge it and try downloading headers again.

Right click/Post Storage/Purge Stored