Mail suddenly not seeing accounts - acting erratically with new ones

When I turned on my Mac and launched Mail, I was prompted with a "Welcome to Mail" screen which would not let me proceed until I setup a new email account.
I have been using 3 accounts on this machine since I got it early this year. They were IMAP accounts, and they were all gone.
So I added one of them back, and then there appeared to be an indexing problem - when I would click on any message after X date in the message list, the wrong message would appear in the preview pane.
After looking online, I moved the Envelope Index to the desktop, which triggered a re-import of the messages. Now the indexing works, but...
At this point, I am not receiving new messages, even when I hit "Get Mail." I know the messages are there, as I see them on my iPhone and they forward to a web mail account.
Any ideas on how to rectify this? I feel like I'm using Windows!

I did some more research and found that it simply won't download any mails beyond UID UID259987-1153548583. So I edited "MessageUidsAlreadyDownloaded2" to tell it that it hasn't downloaded that UID yet, and then told it to check mail again.
The activity window then suddenly sees that it needs to download over 3000 new e-mails... however, it downloads only one e-mail (the one with the UID I mentioned) and then suddenly stops, without downloading the remaining mails.
So I went into Telnet and deleted the e-mail with that UID, and tried again. Nothing happened. I edited "MessageUidsAlreadyDownloaded2" again and now it only downloads mails up to one UID lower than the one I mentioned (UID259986-1153548583).
I deleted a bunch of other messages after the "stuck message" via Telnet too, but no luck so far. So right now there's a gap, like this:
3857 UID259985-1153548583
3858 UID259986-1153548583
3859 UID259994-1153548583
3860 UID259995-1153548583
And Mail.app plain simply refuses to download 3859 and anything beyond that UID.
I'm troubled because this happens with two separate Mail.apps, and I have absolutely no idea how to fix it or what even causes this!

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