I am regularly experiencing situations on my Moodle servers where the Moodle theme (the "out-of-the-box" unmodified Clean theme) on my Moodle 2.7.2 (Build: 20140908) sites don't display correctly. The theme does not render properly and the the YUI/Javascript navigation is broken, e.g. the sections in the Site Admin block do not expand and contract.

It does not appear to be a theme specific problem - the problem occurs on all of the core and non-core themes that I have tried in Moodle 2.5, 2.6 and 2.7. However, I do "suspect" that it is somehow related to the new Moodle Theme engine because I NEVER experience the problem on my old-but-very-stable Moodle 2.0.4 site, so a regression of some kind has sneaked into the modern versions of Moodle.

Searching through the Moodle forums reveals that a lot of people are experiencing similar "theme rendering " problems . See:
https://moodle.org/mod/forum/discuss.php?d=221275
https://moodle.org/mod/forum/discuss.php?d=229775
https://moodle.org/mod/forum/discuss.php?d=231098
https://moodle.org/mod/forum/discuss.php?d=252687
https://moodle.org/mod/forum/discuss.php?d=254959
https://moodle.org/mod/forum/discuss.php?d=255427
https://moodle.org/mod/forum/discuss.php?d=255556
https://moodle.org/mod/forum/discuss.php?d=258830
https://moodle.org/mod/forum/discuss.php?d=261287
https://moodle.org/mod/forum/discuss.php?d=261308
https://moodle.org/mod/forum/discuss.php?d=261982
https://moodle.org/mod/forum/discuss.php?d=263222
https://moodle.org/mod/forum/discuss.php?d=263939
https://moodle.org/mod/forum/discuss.php?d=264337
https://moodle.org/mod/forum/discuss.php?d=265603#p1151050
https://moodle.org/mod/forum/discuss.php?d=266078
https://moodle.org/mod/forum/discuss.php?d=266548
https://moodle.org/mod/forum/discuss.php?d=267990
https://moodle.org/mod/forum/discuss.php?d=268438
https://moodle.org/mod/forum/discuss.php?d=269877
https://moodle.org/mod/forum/discuss.php?d=272469

Determining the cause of this problem is difficult and there appear to be a lot of scenarios that can trigger this, including slow internet or network connections and browser versions, among others. But if it is affecting so many people, then this is surely something that needs to be investigated.

Several workarounds are usually provided in the Moodle forums, most commonly, turning off slash arguments in the Moodle http settings. Running the /admin/purgecaches.php script also seems to temporarily "fix" the problem. But those are not real solutions. That's not getting to, and fixing, the cause of the problem.

I use scorm activities in some of my courses and those activities need slash arguments to be enabled. So turning off slash arguments as a way to 'fix" this is certainly not an option.

I don't use any custom themes or non-core plugins on my production servers, so I can't blame that as the cause of this problem.

https://docs.moodle.org/27/en/Blocks_FAQ#My_Administration_block_links_don.27t_expand.21 doesn't offer a real solution. Disabling and/or enabling the "Use online YUI libraries", "YUI combo loading" and "Cache Javascript" settings does not make a noticeable difference.

I must also add that I have a Moodle 2.0.4 site running on a Windows Server 2003, IIS FastCGI, PHP 5.33 NTS, MSSQL 2008 R2 and SQLSRV production environment and that environment NEVER experiences this problem. But newer versions of Moodle (2.5, 2.6 and 2.7) on my newer Windows Server 2008 R2, IIS FastCGI, PHP 5.4, MSSQL 2008 R2 VM's regularly experience this problem. And it happens with both the SQLSRV and MSSQL drivers and all the recent NTS versions of PHP, including 5.3, 5.4 and 5.5. (I've never tried the thread-safe versions of PHP.)

It is not a browser specific problem - the problem has been reported by my users on multiple Windows browsers, including various versions of Internet Explorer, Firefox and Google Chrome.

Windows only? I don’t know. I don't have any non-Windows Server environments to test on (setting up a Ubuntu test VM is becoming very tempting, but it won't be much use to me since upgrading our Windows servers to Linux is NOT an option).

It's also not PHP version specific. I've experienced this problem on PHP 5.3, 5.4 and 5.5 (all NTS).

I store my Moodledata folder on a NAS device for the production environment. My DEV and QA environments use both the NAS storage and LOCAL storage for the Moodledata folder and the problem is experienced on those VM's that use local storage and also on the VM's that use the NAS storage, so that rules out the NAS storage being the cause of the problem.