diff -up EMBOSS-6.3.1/emboss/tfm.c.fix-doc-finding EMBOSS-6.3.1/emboss/tfm.c
--- EMBOSS-6.3.1/emboss/tfm.c.fix-doc-finding	2010-04-13 10:25:56.000000000 -0400
+++ EMBOSS-6.3.1/emboss/tfm.c	2010-11-04 15:32:45.651745001 -0400
@@ -163,11 +163,15 @@ static void tfm_FindAppDocRoot(const AjP
     /* look at EMBOSS doc files */
 
     /* try to open the installed doc directory */
-    if(ajStrGetLen(roottmp))
-	ajStrAssignS(docroot, roottmp);
-   else
+    if(ajStrGetLen(roottmp)) 
     {
-        ajStrAssignS(&docrootinst, ajNamValueInstalldir());
+	ajStrAssignS(&docrootinst, roottmp);
+	/* Just to be safe. Can't hurt if we end up with multiples here. */
+	ajStrAppendC(&docrootinst,SLASH_STRING);
+    }
+    else
+    {
+	ajStrAssignS(&docrootinst, ajNamValueInstalldir());
 	ajDirnameFix(&docrootinst);
 
 	if(is_windows)
@@ -184,28 +188,28 @@ static void tfm_FindAppDocRoot(const AjP
 	else
 	    ajFmtPrintAppS(&docrootinst, "share%sEMBOSS%sdoc%s",
 			SLASH_STRING,SLASH_STRING,SLASH_STRING);
+    }
 
-
-	if(html)
-	{
-	  if(ajStrGetLen(embassy))
+    if(html)
+    {
+	if(ajStrGetLen(embassy))
 	    ajFmtPrintS(docroot,"%Shtml%sembassy%s%S%s",
 			docrootinst,SLASH_STRING,SLASH_STRING,
 			embassy, SLASH_STRING);
-	  else
-	  {
-	      if(is_windows)
-		  ajFmtPrintS(docroot,"%Sprograms%shtml%s",
-			      docrootinst,SLASH_STRING,SLASH_STRING);
-	      else
-		  ajFmtPrintS(docroot,"%Sprograms%shtml%s",
-			      docrootinst,SLASH_STRING,SLASH_STRING);
-          }
-	}
 	else
+	{
+	    if(is_windows)
+		ajFmtPrintS(docroot,"%Sprograms%shtml%s",
+			    docrootinst,SLASH_STRING,SLASH_STRING);
+	    else
+		ajFmtPrintS(docroot,"%Sprograms%shtml%s",
+			    docrootinst,SLASH_STRING,SLASH_STRING);
+	}
+    }
+    else
 	    ajFmtPrintS(docroot,"%Sprograms%stext%s",docrootinst,SLASH_STRING,
 			SLASH_STRING);
-    }
+
     ajDirnameFix(docroot);
     ajDebug("installed docroot '%S'\n", *docroot);