As usual, after an hours of investigation this issue I make a post only to find the solution a few minutes later.
When I was copying to Dir1 I was creating new files.
When I was copying to Dir2 I was overwriting files that were already moved to the array.
In this case unRAID overwrites the files directly, skipping the cache.
The conclusion is that it's faster to delete the data and create it again than overwriting it.