If you have multiple Windows Settings Groups which capture the following registry setting, in certain scenarios you may experience missing Taskbar pinned items:
This behaviour has been observed as follows:
1. User logs into machine A with an app installed, they pin the shortcut to the Taskbar and log out
2. User logs into machine B without the app installed. Icon is not restored to the Taskbar as expected
3. User logs machine A - the icon is not restored to the Taskbar
This above registry setting should only be captured once for any user. Capturing it multiple times can cause shortcuts to fail to be restored correctly. Ensure it is only included in one WSG, or if it is included in multiple WSGs ensure that only of these WSGs is applied to a Personalization Group to avoid duplication.