FULL PRODUCT VERSION :
java version "1.8.0_101"
Java(TM) SE Runtime Environment (build 1.8.0_101-b13)
Java HotSpot(TM) Client VM (build 25.101-b13, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 6.1.7601]

EXTRA RELEVANT SYSTEM CONFIGURATION :
Any web application server should suffice for deploying a web app that includes a JWS application to test with. I used Tomcat 8.
I used IE 11 to launch the JWS application and reproduce the issue. Chrome can also be used.
I tested with 32-bit JRE 8u101 installed to the desktop, since that is most recent.

A DESCRIPTION OF THE PROBLEM :
Upon executing a Java Web Start (JWS) application from a web server, entries are successfully created in the cache. At some later point, the user can delete the cache entries from the Java Control Panel's "Delete Files..." dialog. The dialog includes 3 checkboxes:
1) Trace and Log Files
2) Cached Applications and Applets
3) Installed Applications and Applets

If the user checks only "Cached Applications and Applets", the cache entries are removed. But if the user re-runs the JWS application, creating the cache entries again, and then deletes files via the JCP, checking only "Installed Applications and Applets", the cached files are removed once again. This is not expected, since the separate checkboxes imply that Cached Applications are distinct from Installed Applications.

The same result occurs if you repeat the test, deleting Installed Applications prior to Cached Applications. The cached entries be removed by selecting only one or the other of these options, but not both.



STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
To test, first remove all cache entries via the JCP, selecting all 3 checkboxes. Next, verify that the entire cache is empty. For example, the following commands will return one line per cache entry. JWS applications will create at least one entry, including a file with a *.idx extension. So you can monitor the entries at any point of time using the following commands from a CMD prompt:

cd /D %USERPROFILE%\AppData\LocalLow\Sun\Java\Deployment\cache
dir /S /B *.idx

Initially, nothing is returned, since the cache is empty. But after executing a JWS application, you will see at least one entry. Then after deleting either Cached Applications or Installed Applications, you will see that once again there are no cache entries.

There may be some JWS applications that are immune to this problem, although I am unaware of any. Unless you have one handy, I recommend deploying one of Oracle's Java Web Start Development Examples, on the following site, to reproduce the issue. I recommend the Dynamic Tree Demo " Deployed Without Codebase", since, as implied, it will deploy to any codebase as is:
https://docs.oracle.com/javase/tutorial/deployment/webstart/examplesIndex.html


EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The cache entries created upon executing a given JWS Application should be deleted from the JCP as either a Cached Application or an Installed Application, but not both.
ACTUAL -
The JWS application cache entry is always deleted from the JCP "Delete Files..." dialog if either the "Cached Applications and Applets" or "Installed Applications and Applets" checkbox is selected.

REPRODUCIBILITY :
This bug can be reproduced always.