The hot cue thing only happens if you load a song from the track skip, keyboard search, or instant doubles, as the player will prioritize the load speed of the song rather that the preference to load your hot cues from the track.
The waveform smoothness issue has more to do with a sync between the display framerate and the song scroll speed, so while it may be a bit choppy for some song playback, try zooming out or changing to a different color view.
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