I have the exact same issue.
French store is my default, and I have english store as well.
When using a browser like a normal user, everything works perfectly.
When trying to force a french URL when using the english store, I get a 404 and vice versa.
Might not look like a big issue and I agree for normal browsing.
What happens is that any english URL, not my default store, cannot be fetched by googlebot. They all get 404.
Looks like Magento is looking for the default store rewrites only.
Any ideas ? Any way to override the Rewrite.php to look for all stores and not only the default store ?
thanks.