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There are two chances :
When you are flashing it might writing file in different allocated slots of memory. or you can say blocks.
or
There can be virus which don't let you delete files from your Memory.
What to do :
In flash tool there is RAM and EMMC test option, try to run that. If you get successful than try to use Format option in flashtool. Format will erase everything so if you dont have preloader file from stock and whole stock ROM to flash , Do not format.
Hope this will help you.
When you are flashing it might writing file in different allocated slots of memory. or you can say blocks.
or
There can be virus which don't let you delete files from your Memory.
What to do :
In flash tool there is RAM and EMMC test option, try to run that. If you get successful than try to use Format option in flashtool. Format will erase everything so if you dont have preloader file from stock and whole stock ROM to flash , Do not format.
Hope this will help you.