Hi,
after I saved the metadata in lightroom and I go back il LRT(3.4), when I click "Auto-transition" it happens this:

   

Sorry, I can't see the problem. Please try initializing again and go through the whole workflow again, like explained in my basic tutorial. http://lrtimelapse.com/tutorial

For example the column of clarity starts with 12 and ends with 0

Probably you did read/ave Metadata from develop module in Lightroom, this wont affect all images, even if selected.

Please make sure to always perform all operations that should affect all images from Grid View (G).

Let me again suggest that you start over the workflow and carefully follow my instructions on http://lrtimelapse.com/workflow or the videos.

thanks!
the problem was that I haven't performed the operations from the grid view!

are you talking about grid view in the devilment module or the library module? Thank You

Grid view (press "G") is always Library.