Having plug-in delay compensation enabled, a track containing the Linear Phase EQ will play back properly. As soon as this track is frozen, the first beats of this track's playback will no longer be in time. It sounds as if plug-in delay compensation has been disabled. This is only true for the first time playback has been started after freezing. From the second time on it is perfectly in time again.
A workaround is to start and stop playback immediately after freezing.