Cloned structures are see though until a block is placed on them

I have a few structures that get filled with air then cloned back from a clone source that acts as a map reset in a mini game I made. This takes a few command blocks with fill followed by clones to work.
When I hit the (map reset) button it works properly even saying it was done in the command feedback lines in the blocks. Parts of the structure appears see through until I place a block and it shows correctly.
This worked just fine before 1.1 but not since.