I keep changing the settings to another image or lower transparency to 0, but the image comes back after every restart.
Odd, it doesn't happen in my machine (classic...)
Which IDE? OS?
I have the same problem:
PhpStorm 2017.1.4
Build #PS-171.4694.2, built on May 16, 2017
Mac OS X 10.12.5
Thats odd!
Clearning does not work either. In reference to the other issue.
macOS 10.12.5
PhpStorm 2017.1.4
Demo:

I understand now, but yeah this is the expected behavior
From the README:
Therefore some things need to be known:
If you rather want to use the IDE's feature, turn off the option in the Material Theme completely. This will prevent the background to be changed at start.
If you want to disable the background completely, set the custom wallpaper path to be empty and the checkbox on, then click Apply, and finally uncheck the option and save.
And same if you want to disable the plugin, it will not revert back the blank wallpaper, you will have to open the IDE's dialog.
Ah, okay! Thanks :)
Where would that setting be? (which one)

Oh yeah I forgot to add the settings to this list as well...
It's on Preferences > Tools > Material Theme > Custom Wallpaper
Thanks! And sorry for the trouble..
This is absolutely my favorite plugin for PhpStorm, thanks for maintaining it 馃憤 !
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Demo: