File Manager Upload Error

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Hello,

I've recently been having problems with I site that we built for our company. The site had worked flawlessly up until a month ago when the site was accidentally wiped out with a web hosting tool. All of our public_html directory and all the databases were deleted. Thankfully we were able to restore from a backup made 2-3 days earlier. The restore was not completely successful and in order to fix some major permissions issues I upgraded to the then-current version (5.6.1.1).

Everything has worked fine, except for uploading files with the File Manager which throws the error:
"Unable to copy file to storage directory. Please check permissions on your upload directory and ensure they can be written to by your web server."

I have tried recursively setting all permissions to 775 and 777 with FileZilla, and I've also tried creating a new files directory and pointing the config at it. None of my "solutions" have worked yet. Does anyone have any suggestions? Is there something that I should be doing differently?

If you need more information please let me know.

Thanks,
Caleb

sagetech