Hello Anders Strand-Holm,
Since the notification count appears correctly as soon as you open Phone Link, I'd like to narrow down whether the issue is with background synchronization or just the taskbar icon updating.
Could you check one thing?
When Phone Link is running in the background and a new message arrives on your Galaxy S25 Ultra, do you still receive a Windows notification banner, even though the taskbar icon doesn't show the count? Or do both only appear after you open Phone Link?
This would help distinguish whether notifications aren't being delivered in the background or whether only the taskbar badge isn't refreshing.
For reference, Microsoft covers Phone Link synchronization and notification behavior here:
https://support.microsoft.com/en-gb/windows/apps/phonelink/troubleshooting-the-phone-link