Alerted by your posts I started to check my power converters, because I didn't used them at my stage of development yet.
And I must say:
1. XL1509-5.0 is a complete piece of crap. Firstly it supposed to give 5V, but it gave 9V. After adding external resistor to its internal voltage divider it gave 5V, but under little current draw (30mA from 3x STM32 and linear regulator) it dropped under 3V.
There was earlier TPS54331. Why you switched to XL1509?
2. I had two days of nightmare with MC34063A. It simply won't switch in boost mode. It only puts thru voltage. I've changed few ICs, but from this same seller. Build another converter. Nothing! It just won't switch.
I've ordered from Ali some assembled converters to swap my ICs and see if they are faulty. Will see.
https://www.aliexpress.com/item/1005002494251409.html
3. I have no issue with -5V yet, but I didn't used it under load.
I smell lithium in the air. It's not lithium, it's glycolium.