I suspect there is a corruption of some kind in rules.ini shipped with some 10.x releases. You could verify this by taking a snapshot of Java JRE using for instance Pictaker 10.5.0.86. The package will be missing every file installed that do not have a file extension!

You should be able to verify this by listing all relevant files on the client and compare to the package:
ls.exe -R -l "%programfiles%\Java" | grep.exe -v "\." >files_with_no_extension.txt

The package will not capture for instance c:\Program Files\Java\jre6\lib\zi\ which contains important time zone information.
Editing the "Ignore Files=" in rules.ini it is possible to do what looks like a correct capture.

Is the statement you shipped to long? Is there a max length for the above entry?
Or is it the repeating file patterns at the end that make Pictaker exclude files without extension? Could you please post a correct rules.ini in 10.5 format?

Thanks!