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Can you try fresh build with latest changes on a fresh install? 
 
I think that problem is with support for resolution/refresh rate changing. Once you change resolution and/or refresh rate, Kodi saves it to configuration file. When you change resolution with script.bin, Kodi will try to set the old one. I fixed fbdev driver, fixed kodi support and yesterday I found out that there is still a bug in mali driver, so I must implement a workaround in Kodi to solve this. 
 
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