I think as others have pointed out, its to do with note order, and the fact there is no live quantisation.
(there are already very long topics about live quantisation, so Im not going into details here)
so, notes will always come in sequentially even when you play a chord.
its only quantisation, that makes chord exactly start at the same time.
and its the quantisation that ‘fixes’ the issue (on the repeat loop)
you can demonstrate this to yourself, by recording a chord, and looking at the micro-time offsets.
the issue here, is the ARP is not quantised nor are the notes, so the ARP starts as soon as it gets the first note, and goes from there, thats why we hear different patterns on the first live input.
you can also see this clearly on the live pads, depending on what pad the Pyramid detects you play first, the pattern will alter the first time around
you can also replicate the issue by programming chords in step mode, and changing the offset ever so slightly, and see how it gets played (with quantisation OFF)
so why the double note??
well, the pyramid sees the lowest note, before its got the other notes… and so is acting as if this is a one note arp… so just plays it again.
now, I should stress this is just what I think happening… so, I do not think its your setup.
BUT Im not saying it’s what I think should happen, similarly, Im not from Squarp , so cannot say if this is intended behaviour.
I think what you need to do is raise it with Squarp via the contact form , and discuss with them, if. they think there is a solution.
I cannot really think of a workaround… other than to use the smart pads (or assign note to smartpad) , these don’t have the same issue, since the chord is see in ‘one go’ - but thats not really a good solution.
so really, your best bet is, as above, to talk to Squarp.