This plugin is quite overzealous when clearing the APC opcode cache, specifically APC's "User Cache Entries". It clears the entire user cache, not just those created by the plugin (those prefixed with w3tc_).
This behavior is detrimental to the other applications on my server which use APC's user cache.
I enjoy using this plugin, but this behavior is a deal breaker, so I hope it will be remedied quickly.
I'm comfortable applying any patches you provide to remedy this issue.