It has been found that if ones run AU on a JRE that has been modified by the FPUpdater tool, the update fails and the user receives a series of error messages:

Here is what Polina found and has been seen by others.
I've just tried:
1. Install 6u20 b02
2. Update rt.jar
3. Java Update to 6u23 - failure
4. Install offline 6u23 b05 - installs and works fine, but need to update rt.jar again

Images of errors attached.
1. Warning: lib/rt.jar: Old File not found. However, a file of the same name was found. No update done since file contents do not match.
2. Error: Java(TM) Update fails to apply changes to your system.
3. Java Setup: Error 1722. There is a problem with this Windows Installer package. A program run as part of the setup did not finish as expected. Contact your support personnel or package vendor.
4. Java Setup: Installation Failed


AU should not fail if it is run against a JRE that has been updated with the FPUpdater tool.