Drupal $custom_theme caching issues?
From my point of view, the better way is to use your own cache system, but don't worry is nothing very complicate.

Copy the includes/cache.inc and put it somewhere in sites/all/libraries or whatever you want. After in your settings.php you've to add $config['cache_inc'] = 'sites/all/...'; and Drupal will replace is own cache system by yours. This file contains three functions, clear_cache_all, cache_set and cache_get. Here the idea is to add the name of your theme before all $cid.

I never tried it, so I'm not sure if you can have access to this informations, but you can try .