Tile Entities in a CLONE ... REPLACE FORCE overlapping region are replaced by barrier blocks on the second clone operation.

The first invoke of CLONE replicates the Tile Entity blocks OK. The second invoke replaces them with barrier blocks. Signs, comparators, command blocks are examples of the affected blocks.

It is a geat feature that works well for regular blocks.

The behaviour can be seen near the end of this video: http://youtu.be/uhpXP1eBhAA