ISRG Root X1 is definetly still part of the Microsoft Root program, and is distributed to all clients where the automatic root update is working. Note that Windows is known to download roots on-demand ("lazy loading"), so ISRG Root X1 is only downloaded upon first visit of a Let's Encrypt-secured website.
There are known cases where the root lazy-loading is not working as intended, see for example here. This can happen if the platform verifier wasn't correctly invoked (some clients don't do this), which prevents the lazy-loading from triggering. The lazy-loading can also fail if the system is unable to download new roots, for example due to network issues (proxy, blocking of MS servers, policy settings...).
There may also be completly unrelated issues with similar symptoms, such as incorrect chains being send (or none at all).