When I run the FileZilla I get this info box.
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FileZilla Portable | PortableApps.com
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FileZilla Portable's settings could not be loaded into the registry.  The account you are logged in with most likely does not have the ability to alter the registry.  FileZilla Portable should still run correctly, but the default settings will be used.
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OK
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I am using admin account and FileZilla worked before. But not anymore. Reinstall did not help.
 
      
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I resolved this issue by deleting /data/settings directory. I actually backed them up and then copied files one by one over fresh installation so I did not lost my settings and everything works smoothly now.
Well done on resolving this yourself and thanks for posting your solution
PortableApps.com Advocate