Thanks for explaining that.
In your first post, you say, "files for powerstore are setup in a sub directory inside the main root directory on the server, they are not actually in the root folder."
But I see that your Admin page is in the root directory of your site (but the Images forder isn't - which is why things look a little different).
You may need to explain the exact structure of your site so we can move forward a bit. All of the Files and folders of PowerStore must be in the same directory, for it to function correctley.
On your Admin page, the menu is missing, whereas on the public areas, (i.e. the 'Home' page the menus are accessible.
As the paths to the menu folder and files are correct in both the Admin page and the public pages, please could you check your Admin pages, and make sure that the paths to your 'Connections/PowerStoreConnection.php' file are correct? On your Admin pages there should be a line near the top of your page:
<?php require_once('../Connections/PowerStoreConnection.php'); ?>
Can you confirm that it looks like that?