So it seems that commits efdff41, cbc33bd, and 8f612c3 were all for naught and the problem may in fact be a bug with Dovecot. I have asked on the Dovecot mailist. Meantime, this is a workaround.

1 files changed, 7 insertions, 3 deletions

diff --git a/roundcubemail/program/include/rcube_imap.php b/roundcubemail/program/include/rcube_imap.php
index e5abe8a5f..c89a4ff4a 100644
--- a/roundcubemail/program/include/rcube_imap.php
+++ b/roundcubemail/program/include/rcube_imap.php
@@ -587,7 +587,7 @@ class rcube_imap
 
     $message_threading = $this->get_capability('thread=references') &&
                          rcmail::get_instance()->imap->threading;
-    $max = $this->_messagecount($mailbox, rcmail::get_instance()->config->get('imap_thread_algorithm'), 'ALL');
+    $max = $this->_messagecount($mailbox, ($message_threading) ? 'THREADS' : 'ALL');
 
     list($begin, $end) = $this->_get_message_range($max, $page);
 
@@ -622,6 +622,12 @@ class rcube_imap
                 } else {
                     list ($thread_tree, $msg_depth, $has_children) = iil_C_Thread($this->conn, $mailbox, rcmail::get_instance()->config->get('imap_thread_algorithm'), 'ALL');
                 }
+
+                // Temporary fix for a possible bug in Dovecot X-REFERENCES2.
+                // Remove this if/when the bug is fixed or the problem solved.
+                if ($thread_tree && array_key_exists(0,$thread_tree))
+                  unset($thread_tree[0]);                  
+
                 $this->update_thread_cache($mailbox, $thread_tree, $msg_depth, $has_children);
                 // the keys of thread_tree are the thread roots
                 $roots = array_keys($thread_tree);
@@ -696,8 +702,6 @@ class rcube_imap
         $deleted_count = $this->_fetch_headers($mailbox, $msgs, $a_msg_headers, $cache_key);
         // delete cached messages with a higher index than $max+1
         // Changed $max to $max+1 to fix this bug : #1484295
-        if ($message_threading)
-            $max = $this->_messagecount($mailbox, 'ALL');
         $this->clear_message_cache($cache_key, $max + 1);
     }