if a blend file was opened with /./ in the path (for example "some/./path/to/./model.blend" ) the relative paths from created from that location would be incorrect. This results in linked library paths being loaded incorrectly.

source/blender/blenlib/intern/util.c

@@ -858,6 +858,8 @@ int BLI_strcaseeq(char *a, char *b) {
  * take the dir name, make it absolute, and clean it up, replacing
  * excess file entry stuff (like /tmp/../tmp/../)
  * note that dir isn't protected for max string names... 
+ * 
+ * If relbase is NULL then its ignored
  */
 
 void BLI_cleanup_dir(const char *relabase, char *dir)
@@ -874,9 +876,9 @@ void BLI_cleanup_file(const char *relabase, char *dir)
 {
 	short a;
 	char *start, *eind;
-	
-	BLI_convertstringcode(dir, relabase, 0);
-	
+	if (relabase) {
+		BLI_convertstringcode(dir, relabase, 0);
+	}
 #ifdef WIN32
 	if(dir[0]=='.') {	/* happens for example in FILE_MAIN */
 	   get_default_root(dir);
@@ -954,7 +956,7 @@ void BLI_makestringcode(const char *relfile, char *file)
 	char * lslash;
 	char temp[FILE_MAXDIR+FILE_MAXFILE];
 	char res[FILE_MAXDIR+FILE_MAXFILE];
-
+	
 	/* if file is already relative, bail out */
 	if(file[0]=='/' && file[1]=='/') return;
 	
@@ -986,7 +988,11 @@ void BLI_makestringcode(const char *relfile, char *file)
 
 	BLI_char_switch(temp, '\\', '/');
 	BLI_char_switch(file, '\\', '/');
-
+	
+	/* remove /./ which confuse the following slash counting... */
+	BLI_cleanup_file(NULL, file);
+	BLI_cleanup_file(NULL, temp);
+	
 	/* the last slash in the file indicates where the path part ends */
 	lslash = BLI_last_slash(temp);
 
@@ -1065,6 +1071,8 @@ int BLI_convertstringcode(char *path, const char *basepath, int framenum)
 
 	BLI_strncpy(base, basepath, FILE_MAX);
 	
+	BLI_cleanup_file(NULL, base);
+	
 	/* push slashes into unix mode - strings entering this part are
 	   potentially messed up: having both back- and forward slashes.
 	   Here we push into one conform direction, and at the end we
@@ -1147,7 +1155,7 @@ int BLI_convertstringcode(char *path, const char *basepath, int framenum)
 	*/
 	BLI_char_switch(path+2, '/', '\\');
 #endif
-
+	
 	return wasrelative;
 }