I think this is because if you open the Tracking Station, it keeps the active vessel loaded, so you can quickly switch back to it if you want, which also means the timewarp stays locked to the active vessel. As a slightly faster workaround than what @Mushylog mentioned, I've found you can accomplish the same effect by going Flight View -> KSC -> Tracking Station instead of just Flight View -> Tracking Station - no need to launch a new vessel.
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