check the module whether is actually loaded

For some reason, the modules in the shared_prefrence are not the same with modules.list.
// for example, reboot too early or other possible problem.
However, the xposed bridge uses the modules.list, and xposed installer use shared_preference.
This patch makes a double check for the enabled modules, otherwise it will make user confused.

The C-part is not the same with Java-part, this is the main cause for MasterKey bug.