I guess I would go through this in baby steps. My next step would be to replace the admin cp on my new 'test' folder with the admin cp on my live site. Then I would try to upload a modification again. See if it works. If not, then you know it is something with the files in the admin cp on your live site. I would keep doing like changes like that to try to figure out what the problem is. Right now, you don't know if it is a database problem or a problem with the files. If you move your database over to the working 'test' site and it is a database problem, then you will still have the same problem.