I have some problem when using the Update manager. Some directories get locked by php-cgi.exe, and thus the replacement of the original directories with the newly downloaded ones (which are fresher) is not successful.
It’s not a permission issue, since modules can be installed via Install from a URL on /admin/modules/install, and that works without problems.

Let’s take an example:

1. Available updates page (/admin/reports/updates/update):

   

   Now I check Select (or other) module to be updated (it doesn’t matter which module I choose, the results are the same!! so it’s just an example).

2. I hit "Download these updates" button.

3. OK, the module’s updated instance gets downloaded without a problem:
   "Updates downloaded successfully":
   

4. Now I click on Continue.

5. Here comes the error. The result:
   "Update failed! See the log below for more information.
   select_or_other

   • Error installing / updating
   • File Transfer failed, reason: Cannot copy D:/Projects/web/drupal-7/tmp/update-extraction-6d8993ac/select_or_other/LICENSE.txt to /Projects/web/drupal-7/htdocs/sites/all/modules/select_or_other/LICENSE.txt."
     

6. OK, I’m starting to try to inspect the possible reasons.

   • Here’s what my Drupal directory structure looks like: . I set ../tmp to be the temporary directory (in /admin/config/media/file-system), the Drupal files are in htdocs. This is correct, as I can install modules via the GUI, as I mentioned above.
   • When I try to enter the htdocs/sites/all/modules/select_or_other directory, I can’t, because I get an "Access denied on file ......sites/all/modules/select_or_other!" when opening in Total Commander, and "...sites/all/modules/select_or_other is not accessible. Access is denied" when opening in Windows Explorer:
     ,
   • OK, I right click the folder, and open Unlocker via its assistant in the context menu. It says this directory is locked by php-cgi.exe:
     
     I click on "Unlock All", and the folder can now get deleted of itself (as it’s not locked anymore by php-cgi.exe), so it simply
   • I can find the updated select_or_other module’s directory in tmp:
     
   • so I have to manually move it to sites/all/modules directory.

What can be the possible reasons of the lockup of the directory by php-cgi.exe? (Maybe Windows Cache Extension 1.1 for PHP 5.3 installed via Web Platform Installer? But if yes, why is that for example the deletion of images or similar via the GUI works correctly?)
What can I do to avoid this problem, and let "Update manager" work?