Broken upload subdirecories

In 2 last releases was broken upload files, that placed in many subdirectories, for example, i have files:
catalog\controller\checkout\cart.php
catalog\model\checkout\order.php
 
I try upload folder catalog, but file doesen't uploaded, but checkout uploading well.

This happen only when file exists in destination (must be replaced).

Anybody help? In 2046 it's didn't work too.

menu: File - Help - Request Support

I using trial version.