I have been trying to get a working thinapp of Java (6 update 37), Firefox (17.0.1 ESR), and Flash (11.5.502) as a single package. I did all the required customization before doing a postscan, and everything worked great. I had issues with Flash not working originally, which were solved by girakul's suggestion here: http://communities.vmware.com/thread/407959?start=15&tstart=0
Then I noticed that Java worked as long as it ran before Flash. If I visited a page with Flash content and then navigated to a page with Java content, the Java content would not load. However, if I deleted the sandbox in the appdata\roaming\thinstall location, Java would again work until the next time a Flash page was visited. I originally considered enabling RemoveSandboxonExit, but the user settings for Firefox are located within the sandbox and I cannot delete them. I even tried using vregtool to compare the contents of the registry.rw.tvr from a clean (Java working) sandbox and a sandbox where Java was broken (as explained by Jason Coleman here: http://virtuallyjason.blogspot.ca/2012/04/messing-with-thinapps-registry-for-fun.html) but was not having any luck.
I was hoping someone may have a suggestion of a setting I could tweak to hopefully solve the issue of Java breaking after Flash is run.
I took the liberty of testing this as another customer brought this to my attention. It seems it's not specifically an issue with Flash or Firefox but rather a Java + UAC issue. I'm making a few assumptions here as everything started working for me when I did the specific "Java 1.6 Tweaks" (also noted in the "How to ThinApp Newer Versions of Java" blog post just prior to step 4).
Specifically, the added Java browser helper objects seem to be causing the UAC issues. Not sure why it only appears after launching Flash first though.
Anyways, I captured the above versions together in a single package on a clean XP SP3 system and after the java tweaks and Flash MMS.CFG settings, was able to get the entire thing working on XP, Win 7 32-bit, and Win 7 64-bit. Even did the "Dirty, Washed, Clean, Production" tests as well and all worked.