Eric .. I'm seeing this on all my sites now - did something change on the upgrade?
These are the settings on HARTmarket.com (root)
>> I set up directories on all my sites and all used to look like this. However, this is what ALL of them look like now - all the subdomains - overrided since the upgrade to v3.8
>> I was able to go into and copy each into the directory e.g. paste /wp-content/blogs.dir/1/files/store/products/images (root site) and change it to /wp-content/blogs.dir/2/files/store/products/images (for beef jerky site) ... but only one at a time to save it. But, then when you come back to the directories and/or hit the "Set up" button it overrides it to these wrong defaults. I'd really hate to have to do that on every store. Is there a way to fix your code?
// added //
It seems to be saving if I SAVE each field individually (4 times) and NOT click the set-up button in the directories section .... At least the field in the Backup directory shows me which blogs.dir/# number it is and I can fix manually. Even the domain mapped domains reverted back to this non-multisite default URL.