Pixel and Tonic graciously made a ticket out of this request and cleared this issue up. (Thanks, guys!)
Here's what Andris had to say:
You have set your upload folder paths to be relative, however when you
access the CP from the address admin.php, those paths turn out to be
For them to work correctly, you must access the CP using the system
folder in path - for example -
In Assets file manager everything was loading fine, because everything
there is loaded via Ajax and Ajax requests are routed via front-end
due to EE's design. Assets compensates for those requests, if they are
made this way.
I was accessing the control panel from
domain.com/admin.php with relative upload paths and I needed to access the control panel from
domain.com/system/ for those paths to work.
Hope that helps anyone else with this issue!