Just to check, is the firmware on your Pico definitely up to date?
I know in the past there was a phase where the Pico/WiFi/etc had some issues with the occasional glitch caused by interrupts during the send process, but I just looked and interrupts do seem to be disabled now
Personally, I would have thought that if the LEDs work and then only flicker some of the time, it may not the actual timing of 1s and 0s that is at fault. It's possible that there is some kind of intermittent timing issue in the data that is sent.
Since you have a scope, I'm not sure if it would have enough sample memory but maybe you could set it to trigger on the waveform so it all gets read in (even if you only send to a handful of APA106), and then just send out data manually until you get the LEDs to display the wrong thing.
When they're displaying the wrong thing, the scope should hopefully have shown the trace and you can see whether everything looks ok (in which case it really is 1/0 timing or electrical) or whether somehow the actual data being sent from Espruino is glitchy.
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