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I would agree that the system cache plugin is the issue. You hav to purge your site's cache before enabling the Javascript combination. Moreover, caching can be set to Off, Conservative or Progessive. Conservative caching should work with the plugin. Progressive, I don't think it should work at all.

Looking at the implementation of the System - Cache plugin in Joomla! 2.5 and 3.0, you can't use it with together with Admin Tools' link migration, force HTTPS and CSS/Javascript combination.

In order for any of those features to work, Admin Tools must be the last thing that runs on the onAfterRender Joomla! event (which it makes sure it does). If it's not the last one, other plugins may end up creating wrong links, non-HTTP links or add more CSS and Javascript files.

In order for the System - Cache plugin to work, it also requires that it's the last thing that runs on the onAfterRender Joomla! event so that it can save the page in the file cache and serve it later from the cache.

No, you can't have Admin Tools' plugin run as the second-to-last onAfterRender event handler. Joomla! implements a FIFO event handling queue. You can only add something to the end of the queue, not in any off place (unless you start modifying the Joomla! core).

So, the bottom line is: Admin Tools SEO & Link features are incompatible with the System - Cache plugin.

Why did it work in Joomla! 2.5? Because you didn't test it thoroughly :) You had enabled the "Use browser cache" feature but you only tried accessing your site from the same browser. If you tried accessing the site from a different browser or device you'd see that it would not be loading the combined Javascript files. Just like your Joomla! 3.0 site (where you didn't use the browser cache option) does.

I am looking at the code in the plugins/system/cache/cache.php under both Joomla! 2.5.8 and 3.0.2. The code is identical. I can actually understand what it does too :) I also understand how my plugin works and how Joomla!'s caching works. Put in layman's terms:

• The System - Cache plugin looks at the page right before it's sent to the browser and saves it to a file
• If that file exists, the next time the page loads it will serve the file and will not let the plugins run
• The System - Admin Tools plugin also needs to take a look at the page right before it's sent to the browser for the features I mentioned in my previous reply to work
• Due to the way Joomla! works, you can only tell it which is the last plugin to take a look at the page before it's sent to the browser. Admin Tools sets itself as the last plugin to take a look at the page before it's sent to the browser. If it didn't, the features I mentioned wouldn't work at all.
• Since Joomla!'s System - Cache plugin takes a look at the page before the System - Admin Tools gets a chance to modify the page, Joomla! caches the "wrong" version of the page, i.e. the page before Admin Tools applies its magic.
• However, the first time you do access the page, Joomla! DOES let all plugins (including Admin Tools) run on the page. This is why you do see the Javascript being combined.
• On the contrary, on the nest page load, the System - Cache plugin kicks in and serves the saved copy of the page. As you remember, it's the copy of the page without Admin Tools' magic applied, i.e. without the Javascript combined.

I would suggest doing the following test with Joomla! 2.5 and, say, Chrome:

• Turn on Admin Tools' Javascript combining feature
• Turn on the System - Cache plugin
• Clear your browser's cache
• Visit a page and take a look at its source code. The Javascript is combined.
• Clear your browser's cache
• Quit the browser. If you're on a Mac use CMD-Q, don't just close all windows
• Restart your browser
• Visit the same page.
• For good measure, do a forced page reload. It's CTRL-SHIFT-R on Windows and Linux, CMD-SHIFT-R on a Mac.
• Take a look at the page's source code. The Javascript is not combined.

I'm terribly sorry to tell you, but your testing is flawed and you get false results. I actually did install fresh copies of Joomla! 2.5.8 and 3.0.2 on a variety of server configurations. In all cases my testing results were identical in both 2.5.8 and 3.0.2 for the very exact reasons I analysed twice above.

However, I understand why you may have mislead. Page caching DOES NOT come into effect in the following cases:

• The cache directory is set incorrectly or otherwise unwritable by Joomla!. In this case nothing can be written to the cache and Joomla! ends up regenerating the page in each page load.
• Debug System is enabled. In this case the System - Cache plugin does not perform any caching to ease debugging the site.
• If you are logged in the System - Cache plugin does not perform any caching. It only caches pages served to guests.

I have spent 6 hours on this non-issue and I am perfectly sure that my analysis from reading the code is 100% verified by the results I get on different browsers, different Joomla! versions and different server environments. From my end this is a non-issue which has to do with Joomla!'s limitations on the plugin queue API. In fact, I would recommend not using the System - Cache plugin as it is hardcoded to always use disk as the caching medium (slow). If you desperately need to speed up your site I would recommend implementing a CDN. There's a great plugin from NoNumber which works with a plethora of CDNs and makes integrating a CDN with Joomla! virtually effortless. Since CDNs read the data which Joomla! would send to the browser the combined CSS/JS does get cached, without the funky effects of the System - Cache plugin.

You're welcome :)