Hi,
It's not because of that extension. That extension works fine on its own. It's because of the customization you made which creates invalid links.
the non-SEF links are like that:
index.php?option=com_hikashop&ctrl=product&task=listing&cid=XXX
That way, you can dynamically change the current category of a listing of products.
However, having that cid parameter in the URL of a products listing should normally never happen and because of that the synchronization system wrongly thinks it is on the product page, not on a listing.
The modifications we made in the file components/com_hikashop/views/product/view.html.php enable the system to have better checks in place to avoid the problem.
The modifications will be included in the next version yes.