Couldn't duplicate your issue, but found several other (possibly 
related) issues with the linked attachment code.  Can verify that 
linked attachments work properly after these changes so closing.

Changes have been made in Git (master):

commit a2f0ad707f3cbca274eadd5ddb41421b959e07a1
Author: Michael M Slusarz <slusarz@horde.org>
Date:   Mon Jul 7 23:52:00 2014 -0600

     [mms] Fix some regressions in linked attachments behavior (Bug #13232).

  imp/docs/CHANGES                                 |   14 ++++++--
  imp/lib/Compose/Attachment.php                   |    6 ++-
  imp/lib/Compose/Attachment/Storage/VfsLinked.php |   38 ++++++++-------------
  imp/lib/Compose/LinkedAttachment.php             |    2 +-
  imp/package.xml                                  |   20 ++++++++++--
  5 files changed, 48 insertions(+), 32 deletions(-)

http://github.com/horde/horde/commit/a2f0ad707f3cbca274eadd5ddb41421b959e07a1

Changes have been made in Git (FRAMEWORK_5_2):

commit b90417d8b4a8cfeef56c6efab385963123cdec5a
Author: Michael M Slusarz <slusarz@horde.org>
Date:   Mon Jul 7 23:52:00 2014 -0600

     [mms] Fix some regressions in linked attachments behavior (Bug #13232).

  imp/docs/CHANGES                                 |    7 ++--
  imp/lib/Compose/Attachment.php                   |    6 ++-
  imp/lib/Compose/Attachment/Storage/VfsLinked.php |   38 ++++++++-------------
  imp/lib/Compose/LinkedAttachment.php             |    2 +-
  imp/package.xml                                  |    2 +
  5 files changed, 26 insertions(+), 29 deletions(-)

http://github.com/horde/horde/commit/b90417d8b4a8cfeef56c6efab385963123cdec5a

Ok, here's the correct pic...

One other thing i noticed, but probably not related: when i attach a 
file, at that time the filesize shows up correctly. After sending, 
when i check the Sent mail folder and the mail i've sent, the 
attachment size is different. I mean incorrect. Smaller than the 
original.

Oh yeah, i see no errors in the logs. At least not related errors, 
sometimes i got a flood of :
EMERG: HORDE [imp] Call to a member function getNamespace() on a 
non-object [pid 18126 on line 503 of 
"/opt/WEBROOT/horde.git/imp/lib/Imap.php"]

But nothing special apart from that. I raised the loglevel to DEBUG, 
but no extra errors  about this.

I can not get the linked attachments to work in latest 6.2.0 IMP. It 
worked in 6.1.5, so i've checked the prefs and the configs, no luck. 
I've sent a mail to the levlist, Michael said it works.
So i did a clean git-install, with clean DB. The only thing i've used 
is the imap-backends config from the live installation. I've upgraded 
pear and php (5.4.4), but in the end i got the same exact 
disfunctioning imp. Attachments always inline in the mail. In the VFS, 
no attachments folder created.
Even better, when i set the $conf[compose][link_attach_size_hard] to 
something else than 0, when i send a mail with attachments, the whole 
horde session dies. It's stuck at sending.

Here is my imp conf.php:
<?php
/* CONFIG START. DO NOT CHANGE ANYTHING IN OR AFTER THIS LINE. */
// $Id: 2f48fe333b68218854ef27745028e6efd3efc6f0 $
$conf['user']['allow_view_source'] = true;
$conf['server']['server_list'] = 'shown';
$conf['compose']['use_vfs'] = true;
$conf['compose']['link_attachments_notify'] = true;
$conf['compose']['link_attach_threshold'] = 5242880;
$conf['compose']['link_attach_size_limit'] = 0;
$conf['compose']['link_attach_size_hard'] = 0;
$conf['compose']['link_attachments'] = true;
$conf['compose']['attach_size_limit'] = 0;
$conf['compose']['attach_count_limit'] = 0;
$conf['compose']['reply_limit'] = 0;
$conf['compose']['ac_threshold'] = 2;
$conf['compose']['htmlsig_img_size'] = 30000;
$conf['pgp']['keylength'] = 1024;
$conf['maillog']['driver'] = 'history';
$conf['sentmail']['driver'] = 'Null';
$conf['contactsimage']['backends'] = array('IMP_Contacts_Avatar_Addressbook');
$conf['tasklist']['use_tasklist'] = false;
$conf['notepad']['use_notepad'] = false;
/* CONFIG END. DO NOT CHANGE ANYTHING IN OR BEFORE THIS LINE. */