Changes have been made in Git (master):

commit 8a58c402595dec789193b6146ec43ebd43ff7c4a
Author: Michael M Slusarz <slusarz@horde.org>
Date:   Sun Mar 23 00:58:50 2014 -0600

     [mms] Fix blacklist/whitelist matching with IMAP backend (Bug #13031).

     Conflicts:
             ingo/docs/CHANGES
             ingo/package.xml

  ingo/docs/CHANGES        |    1 +
  ingo/lib/Script/Imap.php |   20 +++++++++++++++-----
  ingo/package.xml         |    1 +
  3 files changed, 17 insertions(+), 5 deletions(-)

http://git.horde.org/horde-git/-/commit/8a58c402595dec789193b6146ec43ebd43ff7c4a

Ingo 3.1.5

Changes have been made in Git (FRAMEWORK_5_1):

commit 8a4263e4f2b389635c6d1e6fe2af3e5644a27fab
Author: Michael M Slusarz <slusarz@horde.org>
Date:   Sun Mar 23 00:58:50 2014 -0600

     [mms] Fix blacklist/whitelist matching with IMAP backend (Bug #13031).

  ingo/docs/CHANGES        |    1 +
  ingo/lib/Script/Imap.php |   20 +++++++++++++++-----
  ingo/package.xml         |    2 ++
  3 files changed, 18 insertions(+), 5 deletions(-)

http://git.horde.org/horde-git/-/commit/8a4263e4f2b389635c6d1e6fe2af3e5644a27fab

Try this:

<                     if (!$v->getEnvelope()->from->match($addr)) {
<                         $indices = array_diff($indices, 
array($v->getUid()));
<                     }
---

===STEPS TO REPRODUCE===
1. Login to Horde
2. Add one email address to "Mail > Filters > Blacklist"
3. Activate "Preferences > Mail > Filters > 'Apply filter rules upon 
logging on' and 'Apply filter rules whenever Inbox is displayed'"
4. Send email from the same mail address which is in blacklist. Filter 
will work correctly.
5. Now add one more entry to "Mail > Filters > Blacklist" and activate 
the same in step 3.
6. Now send mails with any of the mail address which is in blacklist. 
Filters will not apply for any entry.

===ACTUAL RESULT===

Filters will not apply if more than one entry is in Blacklist filter.

===EXPECTED RESULT===

Filters should apply correctly for all entries in Blacklist filter.

===ROOT CAUSE===

As I understand the issue happens because by some logic matched 
messages are removed from list which for filter should be applied at:

\horde\ingo\lib\Script\Imap.php line 158:

                 foreach ($msgs as $v) {
                     if (!$v->getEnvelope()->from->match($addr)) {
                         $indices = array_diff($indices, array($v->getUid()));
                     }
                 }