I have no idea really as I have very little experience with Drupal, but on reading your post, my first thought is to make sure file permissions are ok.
By downloading files to Win and then reuploading them, it will strip the Linux file permissions (I assume that you reuploaded as root - therefore the 'new' site will be owned by root and the webserver won't have access to it). So to fix this, change the owner to www-data (the default webserver user). You can do this through the Webmin File Manager if you wish (click on the webroot folder in the right pane, then click Info, change owner and make sure you allow it to propergate to all files and subfolders). Or from the commandline (assuming webroot of /var/www/domain1.com):
chown -Rv www-data:www-data /var/www/domain1.com
You may also need to tweak the ownership of the db although I'm not too sure about that (or how you go about it if you do).
I'd check file permissions
I have no idea really as I have very little experience with Drupal, but on reading your post, my first thought is to make sure file permissions are ok.
By downloading files to Win and then reuploading them, it will strip the Linux file permissions (I assume that you reuploaded as root - therefore the 'new' site will be owned by root and the webserver won't have access to it). So to fix this, change the owner to www-data (the default webserver user). You can do this through the Webmin File Manager if you wish (click on the webroot folder in the right pane, then click Info, change owner and make sure you allow it to propergate to all files and subfolders). Or from the commandline (assuming webroot of /var/www/domain1.com):
You may also need to tweak the ownership of the db although I'm not too sure about that (or how you go about it if you do).