Bonjour M. Mrbbp,
1st thought - looking at the schematics w/ the HT16K33 - was VDD 5V...
a) I assume you supply enough of the 5V to the board. I could imagine that there are power spikes / brownouts when starting to send things to the controller... Direct supply from the 5V source may help... Don't know if you need a cap. I'm surprised that it does also not work all the times with a Arduino, when reading your comment correctly. I see though applications working that use only S1 Lithium Battery - 3.7V, max 4.2V when freshly charged -https://learn.adafruit.com/trinket-slash-gemma-space-invader-pendant/wirin
b) Since pins of STN32 on PICO are 5V tolerant, you are fine except may be for the high signal of PICO. I see 10K pull-up resistors of 10K on the LED module: https://learn.adafruit.com/adafruit-led-backpack/downloads - therefore in seams that in no environment a resistor has to be added (but with multiples connected they have to be removed on all but one - best is last in 'chain'). It may be that the high signal and it's flank are not good enough...
d) I do not know about the pin mode PICO is in when just using it straight away without setting. I would expect it to be 'output open drain', but you setting it could help, because I experienced spikes in the past with Espruino's pinMode() - even when it is not changing - but here it IS changing from input to output for the clock and data lines. The issue was then though fixed... a while ago. But I still would give it a try to set pinMode upfront.
e) My last straw would be to put a (Schottky) diodes with ring / cathode (-) towards PICO in the lines to give an extra 0.5..0.7V relieve to the resistors on high signal...
Btw, about a year or two ago I bought this adafruit charlieplex 16x8 LED matrix https://learn.adafruit.com/adafruit-charlieplex-bonnet, but I could not get it properly to display a matching Espruino Graphics display buffer... May be you have done something with that display? I got inspired by you installation with the deer(?) on a tin... and ot is still to come alive for the answer to your flip-dot-generosity!
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