I found the solution to this issue.
If you are rooted, install Xposed and Mohammad Ag's Disable Desk Dock. Solved all my issues.
I think the dev of this module has an Xperia Z1 and has made some of the most amazing and useful modules for Xposed. I highly recommend checking them out and making a donation if you can!
for the first week I use magnetic charging and the issue (self-refresh) not happen. I'm not sure too, but I think some apk from market bring this issue..