From going over the posts it looks to me that there is a problem with where the download folder is being placed. Here are a few rules to keep in mind.
You can only use the above site root option if you install the script in the domains root, meaning mydomain.com. You can not use this option if you install the script into a subfolder of a domain, meaning mydomain.com/smpinstalledhere. The reason for this is that the above site root and in site root options use different methods of finding the proper folder. The above site root uses file paths like /users/myusername/public_html/somefolderhere/ and the in site root uses domain urls like mydomain.com/smpinstalledhere/downloadfolder/.
You can not have the download folder anywhere but as a sub folder of SMP, unless you are using the above site root option.
You cant install SMP in mydomain.com/smpinstalledhere and have the download folder in mydomain.com/mydownloadfolder. It would have to be located as mydomain.com/smpinstalledhere/mydownloadfolder to work.
Another thing to keep in mind. If you are using the in site root option you only put the download folder name in the box. This means if your folder is located at mydomain.com/smpinstalledhere/mydownloadshere then the only thing you put in the box would be mydownloadshere.