When a file is placed into an ibay directory it needs to have the correct perms for user and group.
My index.html file in my Primary ibay looks like:
-rw-r----- 1 admin shared 202 Feb 16 2002 index.htm
This equates to user=admin, group=shared, permissions are owner=rw, group=r - BTW use Midnight Commander (mc at the prompt) for an easy way to access and manipulate this info.
The best way to update this is to change the ownership in the SME panel to something else. save, then change it back, save - all files and folders have their perms and ownership reset.
Be careful of any php directives that may be related to the previous location of the files and update as needed.
HTH