I have the same issue and have discovered it is tied to the shortcode uploader when using a specific gallery id. if I use [ngg_uploader id=1] or something with the id every file uploaded returns “is not a valid file” if I just use [ngg_uploader] then I get the success message and no error message.
Since I don’t want my users to upload every image into one default gallery I need this solved.
Allstra I really wish you would post your npu_upload.php file for us as I am not a coder and can’t find the echo’s (hell I don’t even know how to spot one). Any help here guys would be awesome for those of us stuck on this one.