In the combined sequencer and arpeggiator mode (aka the Matrix Arpeggiator, MxArp for short hereafter), no notes are stored and the blue lights are not sequence notes as such and not semitones, but instead octave selections for the up to 4 held keys. The MxArp is not adequately described in the manual and it may not be entirely intuitive...
One thing that will put the blue lights (octave selections) into the progression you see, is if you've been in MxArp mode, the go to sequencer mode, then back to MxArp mode. That is intentional - it's an MxArp reset (not mentioned in the manual). BTW, if you start in MxArp mode, hold some notes and then go to sequencer mode, the MxArp pattern that was playing will be captured to the sequencer (not mentioned in the manual). Mind you, there's sometimes an issue where you get a scrambled MxArp pattern when you have been in sequencer mode and go back to MxArp mode, but I can't get that to happen as I'm testing right now (rare occurrence anyway).
If you get a different tonality/sound/tempo, as you describe, that could be due to panel knobs being detected in their physical position as the synth warms up and things are drifting slightly. If you select a preset right after power up and let it stay at that preset, it may be changed in this way during warm up and thus sound different. A good practice to avoid this is to select a/the preset after the warm up period. I consider the warm up period to be around 20 minutes, and if I want to do an for autotune I wait at least 30 minutes (as an side, haven't needed an autotune in two years - it just stays in tune, but that's ion the same room not being moved).
Another potential gotcha for getting a "surprise" tempo is if the setting in the MCC for "Load Sequence Tempo" is set to "never", whereby the tempo becomes global in the sense that new tempos are not loaded when a preset is loaded. However, I doubt that is part of your issue.
So apart from the panel knob drift during warmup and the Tempo Loading setting, I can't think of any known things that might change your sound and tempo. I've just been playing around a bit with the MxArp, and don't get any strange things happening here. I've not power cycled cold/warm states though - if I did that I'd expect the odd panel knobs physical position to take effect during warmup, as described. If you continue to get unexpected changes other than those I've mentioned in this posting, I'd recommend a chat with tech support.
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