I created an work-arround the bug here with the following patch:

diff --git a/ActiveSync/SOGoActiveSyncDispatcher.m b/ActiveSync/SOGoActiveSyncDispatcher.m
index 83314be..e82ec95 100644
--- a/ActiveSync/SOGoActiveSyncDispatcher.m
+++ b/ActiveSync/SOGoActiveSyncDispatcher.m
@@ -704,6 +704,7 @@ static BOOL debugOn = NO;
SOGoCacheGCSObject o;
id currentFolder;
NSData d;

• NSMutableDictionary *processedFolders;

  int status, command_count, i, type, fi, count;

@@ -849,6 +850,8 @@ static BOOL debugOn = NO;
}
}

• processedFolders = [NSMutableDictionary dictionary];
  // Handle addition and changes
  for (i = 0; i < [allFoldersMetadata count]; i++)
  {
  @@ -862,7 +865,11 @@ static BOOL debugOn = NO;

  serverId = [NSString stringWithFormat: @"mail/%@", [[imapGUIDs objectForKey: nameInCache] substringFromIndex: 6]];
  name = [folderMetadata objectForKey: @"displayName"];

• if ([[processedFolders objectForKey:serverId] intValue] == 42)
• continue;
• [processedFolders setObject:[NSNumber numberWithInt:42] forKey:serverId];

• if ([name hasPrefix: @"/"])
  name = [name substringFromIndex: 1];

Why 42? Because it is the "Answer to the Ultimate Question of Life, The Universe, and Everything".

On my MySQL database the folder list is not duplicated. sogo-tool and the web interfaces will also show a correct folder list.

Config file at the time: http://pastebin.com/71jy2zZC