Hi,

Could you try the attached patches and see if they solve your issues?

Thanks,
Rasmus

-- 
C is for Cookie
>From 8951c689a7812d6557ba65888e549013814e5f8a Mon Sep 17 00:00:00 2001
From: Rasmus <ras...@gmx.us>
Date: Wed, 15 Apr 2015 21:50:53 +0200
Subject: [PATCH 2/2] ox: Change label naming scheme

* ox.el (org-export-get-reference): Change labeling scheme.

160820bc94 and later changed the label naming scheme to follow types.
This commit maps to types to more standard names, e.g. 'headline' to
'sec'.
---
 lisp/ox.el | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/lisp/ox.el b/lisp/ox.el
index d6dcc82..f7d0ef5 100644
--- a/lisp/ox.el
+++ b/lisp/ox.el
@@ -4149,9 +4149,18 @@ alphanumeric characters only."
 		     h))))
     (or (gethash datum cache)
 	(puthash datum
-		 (format "org%s%d"
+		 (format "%s:%d"
 			 (if type
-			     (replace-regexp-in-string "-" "" (symbol-name type))
+			     (case type
+			       (headline "sec")
+			       (paragraph
+				(if (org-element-property :caption datum)
+				    "fig" "paragraph"))
+			       (latex-environment "eq")
+			       (table "tbl")
+			       (otherwise
+				(replace-regexp-in-string "-" ""
+							  (symbol-name type))))
 			   "secondarystring")
 			 (incf (gethash type cache 0)))
 		 cache))))
-- 
2.3.5

>From a01e6759a6a016fd4c684eaaa56544d8507c897f Mon Sep 17 00:00:00 2001
From: Rasmus <ras...@gmx.us>
Date: Wed, 15 Apr 2015 21:46:57 +0200
Subject: [PATCH 1/2] ox-latex: Wider user-label support

* ox-latex.el (org-latex--label): Add user-labels for targets and
  radio-target.
(org-latex--wrap-label, org-latex-link, org-latex-target)
(org-latex-radio-target): Use org-latex--label.
---
 lisp/ox-latex.el | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/lisp/ox-latex.el b/lisp/ox-latex.el
index 61d16b1..b22b0a7 100644
--- a/lisp/ox-latex.el
+++ b/lisp/ox-latex.el
@@ -1056,9 +1056,10 @@ return a unique label.
 Eventually, if FULL is non-nil, wrap label within \"\\label{}\"."
   (let* ((user-label
 	  (org-element-property
-	   (if (memq (org-element-type element) '(headline inlinetask))
-	       :CUSTOM_ID
-	     :name)
+	   (case (org-element-type element)
+	     ((headline inlinetask) :CUSTOM_ID)
+	     ((target radio-target) :value)
+	     (otherwise :name))
 	   element))
 	 (label
 	  (and (or user-label force)
@@ -1176,7 +1177,7 @@ should not be used for floats.  See
   (if (not (and (org-string-nw-p output) (org-element-property :name element)))
       output
     (concat (format "\\phantomsection\n\\label{%s}\n"
-		    (org-export-get-reference element info))
+		    (org-latex--label element info))
 	    output)))
 
 (defun org-latex--text-markup (text markup info)
@@ -2088,7 +2089,7 @@ INFO is a plist holding contextual information.  See
       (let ((destination (org-export-resolve-radio-link link info)))
 	(if (not destination) desc
 	  (format "\\hyperref[%s]{%s}"
-		  (org-export-get-reference destination info)
+		  (org-latex--label destination info)
 		  desc))))
      ;; Links pointing to a headline: Find destination and build
      ;; appropriate referencing command.
@@ -2416,7 +2417,7 @@ holding contextual information."
   "Transcode a RADIO-TARGET object from Org to LaTeX.
 TEXT is the text of the target.  INFO is a plist holding
 contextual information."
-  (format "\\label{%s}%s" (org-export-get-reference radio-target info) text))
+  (format "\\label{%s}%s" (org-latex--label radio-target info) text))
 
 
 ;;;; Section
@@ -3029,7 +3030,7 @@ a communication channel."
   "Transcode a TARGET object from Org to LaTeX.
 CONTENTS is nil.  INFO is a plist holding contextual
 information."
-  (format "\\label{%s}" (org-export-get-reference target info)))
+  (format "\\label{%s}" (org-latex--label target info)))
 
 
 ;;;; Timestamp
-- 
2.3.5

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