Styles gone after clearing the caches

Hi,

I have a long-standing problem with Fusion-based sub-themes, including unmodified packages like 'Acquia Slate' and own sub-themes, but I don't know to what degree Fusion is actually involved since I don't have any similar complex themes to compare; however, with an unmodified 'Garland' I don't encounter this issue; also, with other base themes like 'Zen' or 'Adaptivetheme' I never experienced this, but I havn't used them so intensively like 'Fusion'. Probably other JS-heavy modules (like Panels) or even Drupal core might be involved; and this has definitely something to do with caching and JS aggregation. I suspect Fusion because Fusion does some CSS related preprocessing in template.php (./sites/all/themes/fusion/fusion_core/template.php) I don't fully understand.

The problem: After clearing the Drupal caches (e.g. via 'admin_menu' or 'drush cc'), I get an unstyled display of the website (pretty much like this: example from advagg). The affected page has a reference to the CSS stylesheet and JS file, e.g.:

<link type="text/css" rel="stylesheet" media="all" href="/sites/default/files/css/css_b38e1e19abb231a3c8740b56fd4db339.css" />

If I inspect this in Firebug/Dragonfly, the referenced files like ./sites/default/files/css/css_b38e1e19abb231a3c8740b56fd4db339.css or ./sites/default/files/js/js_3e70254cea4393260c64191e6f37606e.jsmin.js does not exist; probably they were purged by clearing the caches, and for whatever reason the aggregated files seem not to be regenerated, or the references are not being refreshed. The ugly thing with this is that I have no idea to fix this since clearing the caches causes the problem. I believe the issue disappears after a while, but I don't know when and how. I watched an affected site for a couple of hours, and the broken references to the CSS and JS files were still there. On sites where I use boost, it helps to completely wipe the static 'boost' cache. Obviously this is not a really viable option, and the issue also occurs on sites without boost.

The behaviour affects anonymous user, but not user #1 or other logged-in users. What makes this a real pain in the a** is that the issue is not 100% reproducable. E.g. I had this for months on a site with 'Acquia Slate', but for some reason it suddenly disappeared when I just checked. It usually occurs on the frontpage and not on sub-pages; my front pages are usually made with Panels, but other Panels pages are not necessarily affected (in the Panels queue is a long-standing and obscure issue with panels pages as Drupal frontpages). Or it simply only the first page loaded after clearing the caches is affected, I'm not sure. However, in most cases I can reproduce the problem on the front page.

Except for Drupal core's caching mechanisms, other modules that might be involved include panels, jQuery Update, jQuery UI, css_gzip, javascript_aggregator, boost, and probably even more.

I'm posting this as a support request to find out if this is a known issue, or if this only affects a special type of setup I'm using on all my sites. When digging in the issue queues of the mentioned modules, I stumbled over a whole hornet's nest of somehow related issues that are vastely beyond my understanding.

For example there is #1150150: AdvAgg - Fusion Core theme - Lost local.css? and #1154732: AdvAgg Integration with a Fusion-related issue that affects the 'Advanced CSS/JS Aggregation' module; most bizarrely, this module claims to solve issues with broken references to CSS/JS files that come with CSS/JS aggregation: "...getting a 404 for a CSS or JS file is now almost impossible".

Anyway, I'd love to get any pointers how to resolve this. Please feel free to change the issue queue if you know a more appropriate one.

Thank you!