My understanding:
The track Waves VU is using REAPER's anticipative FX processing which at the default 200 ms render ahead setting (see in Preferences/ Audio/ Buffering) is allowing 200ms look ahead to process the FX audio, but the FX graphics (meter) is triggered immediately this anticipative processing starts; the graphics are not delayed.
Anticipative FX processing doesn't happen on the master track, so the graphics will be in time with the audio. What you're seeing (relative to what you hear) is not the master Waves VU late, but the track Waves VU early.
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