With that many things going wrong, I'm wondering if your pan config is
corrupted. I'd also check your disk/ssd's SMART report, to be sure that
isn't failing, and run various system diagnostics to be sure you're not
getting power brown-outs and the like, and maybe a memory diagnostic as
well, tho if pan's the /only/ thing acting up the system's likely fine,
but it can't hurt to check.
Assuming nothing appears outright corrupted (no binary gibberish in the
middle of a text file, etc), I'd ensure I had a backup of my pan settings,
then either start clean and reconfigure, or if it's less work, start clean
and restore the config from backup a file or a few at a time. Luckily
most of pan's config is text-based, with the files named such that it's
fairly easy to see what each one does. (An exception is the newsrc files
which track groups on each server along with the per-server per-group
read-message sequence numbers. They're identified with a number and
newsrc, with the mapping of which one goes to which server in the
servers.xml file.)
What I'd probably do here is restore the general settings files such as
preferences.xml and the hotkeys files (if you've customized hotkeys), and
ensure that they seem to be fine before actually starting on the server
config, which I'd probably redo from scratch. The subscribed groups could
go either way. Then one by one I'd move the old newsrc files in place,
manually editing the servers.xml file to map them as appropriate, so as
not to lose the read-message tracking. Tho the newsrc files could well be
part of the problem -- perhaps the mapping between server and its newsrc
file, as stored in servers.xml, got screwed up. So you may need to dump
the newsrc files and start over with that bit of the config, downloading
the list of groups from each server again to initialize new newsrc files,
and starting over with marking which messages you've already read.
Your posting.xml file, which tracks the posting profile settings, could
also be messed up, so you might need to rebuild your posting profiles from
scratch.