**MacGyver Solution:**

Make a copy/backup from file `Export Layers to Files.jsx`, available on your Photoshop CS6 instalation folder (`C:\Program Files (x86)\Adobe\Adobe Photoshop CS6\Presets\Scripts`).

Edit the file (using notepad or whatever...) and comment/change line 940 (or use the find text tool):

    obj.artLayers[i].remove();

to:

    //obj.artLayers[i].remove();


Save file and use it on Photoshop. `File` > `Scripts` > `Open File/Load script`
This worked great for me. Much faster.