System etc.

Windows 7 Home Premium, Service Pack 1, 64 bit
Cygwin 1.7.17-1
GNU Emacs 24.2.1(i686-pc-cygwin, GTK+ Version 2.24.11) of 2012-08-27 on 
fiona
Org-mode version 7.9.2 (release_7.9.2-646-g664217 @ 
/home/Charlie/elisp/org-mode/lisp/)
updated using the following make autoloads && make update

Up until the past week or two, whenever I updated from git, even when no 
.el files were changed, the org manual was always "remade", "retypeset" 
and  other info or TeX files as well.

For my most recent update I decided to create a log (attached) and 
noticed permission denied for some files concerning org.t2d.

Also attached is a list of files in the ~/elsip/org-mode/doc directory.

I have cc'd Achim Gratz in case this is a cygwin related problem (at 
least it is my impression that Achim also uses cygwin .) I have not 
downloaded emacs-24.2.90-1; however all other packages were updated 
(including the AucTeX).

If this is not a bug, just point me in the correct direction so I can 
solve this.

TIA.

Charlie Millar