I have a WordPress Multisite installation which uses subfolders (ex. "/fr", "/us") for different languages (and different content).
Once I installed v.4.5.03, the main site works fine, but the subsites show a 404 for every page, and the Settings | Permalinks don't show the /xx subsite slugs anymore.
Furthermore, each subsite show all the main site's pages and articles, and not their own content.
For now, I've reverted back to your previous stable 4.4.x version.