All customisations are lost occasionally. This happens only when using memcached, not with APC. The most visible problem is the default sidebar which gets stuck in the cache when this happens. I have no idea how to debug this, but I've implemented a workaround which throws an exception if bad sidebar is detected before it is cached.
There doesn't seem to be any pattern on the requests on which this appear, they all have same backtrace to the sidebar:
#0 /var/www/w/includes/SkinTemplate.php(472): Skin->buildSidebar()
#1 /var/www/w/includes/OutputPage.php(1171): SkinTemplate->outputPage(Object(OutputPage))
#2 /var/www/w/includes/Wiki.php(356): OutputPage->output()
#3 /var/www/w/index.php(118): MediaWiki->finalCleanup(Array, Object(OutputPage))
#4 {main}
Version: 1.16.x
Severity: major