wlord,
The problem was not with you, but from incomplete (and therefore misleading) information online. There are some pages on the web claiming that DokuWiki users can replace the default logo by simply uploading their logo through the "Media Manager". However, these pages neglect to mention that this is ONLY true for "open" DokuWiki sites. When attempting this in a "closed" DokuWiki site (where the ACL is set to "None" for the "@ALL" group), the new logo will not appear on the "Login" screen (which will reflect a "broken" graphic link... or nothing at all where the logo should appear). The logo only appears after login. So to make your DokuWiki site look as it should, always upload your logo into the proper TEMPLATE folder.
By default, most DokuWiki templates are designed to use a file named "logo.png" from the template sub-folder titled "images". To change the logo, rename your company/organization logo to "logo.png" and upload it (via FTP) to the "images" folder of the template you're using. For example, to change the DokuWiki logo within the standard DokuWiki template to your own, upload your company/organization "logo.png" file to the "
http://www.YOUR-DOMAIN.com/dokuwiki/lib/tpl/dokuwiki/images/" folder.
An exception to the above includes the "Monobook" and "Vector" templates, which store ALL user files in a common location. So to change the logo in those templates, upload your company/organization "logo.png" file to the "
http://www.YOUR-DOMAIN.com/dokuwiki/lib/tpl/monobook/user/" (or "
http://www.YOUR-DOMAIN.com/dokuwiki/lib/tpl/vector/user/") folder - as appropriate. The space allowed for a logo in some templates is limited (the default DokuWiki logo is 128x128px, so your logo should be of a similar size).