I am having a similar problem. I use the excellent update manager on several sites and it performs perfectly on all except one.
The problem site throws the following error message
" * Unable to write entry
Warning: file_put_contents(/home/joomla15/public_html/templates/rhuk_milkyway/css/template.css) [function.file-put-contents]: failed to open stream: Permission denied in /home/joomla15/public_html/libraries/joomla/filesystem/file.php on line 298
Failed to extract archive!"
I took a look at the file.php file but my php knowlegde is limited and I couldn't see where the problem may be.
If anyone has any ideas or suggestions it would be greatly appreciated thanks.
Happy New Year
Graham