A Clover-for-IDEA plug-in works correctly with IDEA 12 official release. However, you have ensure that the new "external build" feature is disabled. Open File > Settings > Project Settings > Compiler and un-check the "Use external build" toggle (CLOV-1186).
This release contains no fixes related directly with IDEA plug-in. However, there were changes in Clover core - see the Clover-for-Ant Changelog.