Aggregated CSS & JS files revert to old version
Couple things to look into. An external cache (Varnish/Boost/etc...) could be referencing the old files. This issue will help with the variable_set's with css/js aggregation https://www.drupal.org/node/886488#comment-9668583. Also see this issue: https://www.drupal.org/node/1014086. I'd guess it's an external caching issue based off of what your describing but I can't say for sure due to the flaws in core that have still not been fixed.

In all honesty advagg will fix these issue for you. Drupal.org uses it due to issues with deployments https://www.drupal.org/node/1412130 https://www.drupal.org/node/2446971