Greetings.
I got sup working with one POP3 account, but somewhere along the line it stopped putting messages into the index while I was adding a second account.
I can manually see the messages in the correct maildir folders, but '$ sup-sync' reports "0 messages scanned..."
Running sup in debug mode reports that polling turns up 0 messages too.

debug output:
[2014-11-18 22:54:16 -0500] trying to acquire poll lock for: maildir:/home/user/Mail/william@domain1.com...
[2014-11-18 22:54:16 -0500] lock acquired for: maildir:/home/user/Mail/william@domain1.com
[2014-11-18 22:54:16 -0500] polling maildir /home/user/Mail/william@domain1.com/cur
[2014-11-18 22:54:16 -0500] polling maildir /home/user/Mail/william@domain1.com/new
[2014-11-18 22:54:16 -0500] 0 added, 0 deleted, 0 updated
[2014-11-18 22:54:16 -0500] lock released for: maildir:/home/user/Mail/william@domain1.com
[2014-11-18 22:54:16 -0500] trying to acquire poll lock for: maildir:/home/user/Mail/william@domain2.com...
[2014-11-18 22:54:16 -0500] lock acquired for: maildir:/home/user/Mail/william@domain2.com
[2014-11-18 22:54:16 -0500] polling maildir /home/user/Mail/william@domain2.com/cur
[2014-11-18 22:54:16 -0500] polling maildir /home/user/Mail/william@domain2.com/new
[2014-11-18 22:54:16 -0500] 0 added, 0 deleted, 0 updated
[2014-11-18 22:54:16 -0500] lock released for: maildir:/home/user/Mail/william@domain2.com
[2014-11-18 22:54:16 -0500] trying to acquire poll lock for: sup://drafts...
[2014-11-18 22:54:16 -0500] lock acquired for: sup://drafts
[2014-11-18 22:54:16 -0500] lock released for: sup://drafts
[2014-11-18 22:54:16 -0500] trying to acquire poll lock for: sup://sent...
[2014-11-18 22:54:16 -0500] lock acquired for: sup://sent
[2014-11-18 22:54:16 -0500] benchmark mbox_read_index:   0.000000   0.000000   0.000000 (  0.000045)
[2014-11-18 22:54:16 -0500] lock released for: sup://sent



config.yaml:
---
:editor: "/usr/bin/nano"
:thread_by_subject: true
:edit_signature: false
:ask_for_from: true
:ask_for_to: true
:ask_for_cc: true
:ask_for_bcc: false
:ask_for_subject: true
:account_selector: true
:confirm_no_attachments: true
:confirm_top_posting: true
:jump_to_open_message: true
:discard_snippets_from_encrypted_messages: false
:load_more_threads_when_scrolling: true
:default_attachment_save_dir: ''
:sent_source: sup://sent
:archive_sent: true
:poll_interval: 300
:wrap_width: 0
:slip_rows: 0
:col_jump: 2
:stem_language: english
:sync_back_to_maildir: false
:continuous_scroll: false
:always_edit_async: false
:accounts:
  :default:
    :name: William
    :email: william@domain1.com
    :sendmail: msmtp -t --read-envelope-from
    :signature: "/home/user/.signature"
    :gpgkey: ''
    :alternates: []
  :williambitmessage:
    :name: William
    :email: william@domain2.com
    :sendmail: msmtp -t --read-envelope-from
    :signature: "/home/user/.signature"
    :gpgkey: ''
    :alternates: []
:time_mode: 24h

sources.yaml:
---
- !supmua.org,2006-10-01/Redwood/Maildir
  uri: maildir:~/Mail/william@domain1.com
  usual: true
  archived: false
  sync_back: true
  id: 1
  labels: []
- !supmua.org,2006-10-01/Redwood/Maildir
  uri: maildir:/home/user/Mail/william@domain2.com
  usual: true
  archived: false
  sync_back: true
  id: 2
  labels: []
- !supmua.org,2006-10-01/Redwood/SentLoader {}

As you can see, I tried with both "~/..." and the literal "/home/user/..." paths in sources.yaml. Both accounts have messages waiting in /home/user/Mail/<email_address>/new
Should I just try for a reinstall, or is there something obviously wrong with my config files?