You mentioned using a very high buffer setting for live performance stability. Does the problem go away with a more 'normal' ASIO buffer setting (e.g. 64-256 samples)?
Does it affect a new project with no plugins in it (disable Stop At Project End in Track View Options to be able run the Playback metronome with no content). If not, some plugin and/or the delay compensation in affected projects may be causing a problem.
To help find where this is occurring, put a send on the Metronome bus to an Aux track, and record it. Then zoom in and check whether the 1:01 transient matches the 2:01 transient for amplitude and timing. If it does, invert the phase on the recorded track, and see if all clicks null with the live metronome output.
- If all do, then we know the attenuation is affecting all audio output at 1:01:000, not just the metronome.
- If none do, you might need to dial in your record latency compensation.
- If only the first click fails to null... I'll have to think some more.
P.S. Another thing to check: Does it affect a 48 kHz project the same as 44.1 kHz?