ltwally
The ibay subfolders /files, /html, /cgi-bin, are hidden (by the system) when the ibay is configured to NOT have internet access, so when browsing shares using Windows Explorer etc, your data files will appear to be in /ibay, but they are actually in /ibay/files.
If you take a look using the Linux command prompt, all the subfolders are still there and data files will be located in the /files subfolder.
When you enable Internet access to the ibay, then the subfolders are no longer hidden, so with Windows file sharing/Windows Explorer you WILL see .../ibay/cgi-bin, .../ibay/files, & .../ibay/html.
To be directly accessible via Internet using the URL
www.yourdomain.com/ibayname, any data &/or web files should be in the html folder rather than the files folder.
Note you can access data files that are in the /files subfolder using the Internet URL of
www.yourdomain.com/ibayname/filesYou say:
"When we browse ibays using Windows clients, some ibays point to the /files directory of the ibay, while other ibays point to the ibay directory."
"In this example, both ibays are using the same settings"
I would have said that the ibay settings must be different, ie one has Internet access enabled and the other has internet access disabled, that is theoretically the only reason why you should see differences in folder/file location.
If it's not behaving that way, then perhaps you have found a bug and should report it to bugzilla.