there is only 1 web.config in the package these days if you used one named fulltrust then its an old one, you must use the new one which has no references to NeatUpload and its a good idea to delete the Brettle.Web.NeatUpload.dll from the bin folder just to make sure it is n't interfering.
See also the article Supporting Large File Uploads which has all the information I know for troubleshooting upload problems.
all web browsers have built in dev tools, how you get to it depends on which browser you are using, IE for example the F12 key opens dev tools, then you need to look in the console for script errors
good idea to review important skin changes because old skins probably need the jquery migrate plugin enabled to fix script errors. any script error on the page even if unrelated to the new file uploader will break it.
you might also try uploading on our demo site to see how it is supposed to work to better know what it is not doing on your site