You need to have write permissions to the Scripts directory (eg. /Applications/Adobe After Effects CS5.5/Scripts) in order to install the Qube AR submission scripts. Unfortunately, AfterEffects doesn't seem to use a user-based scripts directory, only the one under /Applications, which are usually read-only to non-root users.
I'm going to log a bug for this one; the GUI should automatically try and open the permissions up on that directory before it writes to it.
For now, you need to open/set the permissions manually from a Terminal window:
sudo chmod 777 /Applications/Adobe After Effects CS5.5/Scripts
(substitute CS6 for CS5.5 as applicable), then use the QubeGUI to install the scripts, then set the permissions back to read-only with
sudo chmod 755 /Applications/Adobe After Effects CS5.5/Scripts