This is an old post, so I assume the issue has been resolved, but it’s being surfaced through search engines so I want to add a comment.
This is my approach from a theme support perspective:
The chances of the original theme causing this issue is nil. It is not possible.
The problem will be caused by Shopify, an app, or custom code.
In terms of tracking down the cause, the first thing I’d want to know is if this is a back-end or front-end issue.
If the collection’s sort order changes in the collection-edit admin page, then that’s a back-end Shopify issue. Themes can’t change how your collection is configured, they can only present what is set up in Shopify. Only Shopify itself & apps can change your collection the way it appears in the admin side.
If this is the case, and your collection sort order is changing in Shopify’s admin pages, then you’ll need to run through any apps you have installed that could rearrange/re-sync your products and talk to their support teams. Shopify’s support may also be able to help.
If the collection looks fine, and the issue is purely with how it displays on the storefront, then the most likely cause of this issue is any app installed for filtering & search. These often fully replace the collection page product grid with their own display logic.
If an app is used for this purpose, you can talk to the app’s support team about this issue.
If it’s a front-end issue, and no apps are being used, then the next thing to do would be to check if the same issue occurs in a free theme (like Dawn). This will determine if the issue is caused by a bug in Shopify’s Online Store.
If it’s a front-end issue, and it looks fine in Dawn, the next step is checking an unmodified version of the theme (Expression), which can be installed from the Theme Store. This is an attempt to rule out custom code added to the theme. If it still fails in an unmodified copy of the theme, then you can talk to the theme’s support team for more advice.
These are the steps we’d go through if you contacted our theme’s support team, and hopefully this might save someone some time finding the right person to talk to (and solve the problem) if they run into the same issue.