This is the symptom of a permission problem.

The "configuration.php" file is probably protected that may explain the permission issue.
In addition, it seems that JMS was not able to perform a backup of some files to restore them in case of rool back.
JMS contain 3 backups of the files that are patched.
- The first backup is performed when you install JMS. The directory is backup_on_install
- The second backup is performed when you try to install the patches. The directory is backup;
- Finally, JMS contain a copy of the original Joomla files in several version (from J1.5.3 to 1.5.11) in aim to roolback the original files in case of problem.

So the problem in your case is to identify the reason why the "configuration.php" present in the master website can not be patched.

Sometime to bypass the permissions problem you can use the Joomla FTP Layer.
See tutorial step 15.