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Thanks everyone, safe boot procedure by holding pin 12 high during reset completely solved my problem!
@daniel the failure is on the first wake-up. I don't have a multimeter handy, but can do that this evening.
I added @jojo suggestion and the board wakes now. I have left it in a sleep wake cycle and will see how long it runs.
I don't know of any alternative, but have you tried it on another computer?
Hmm ok I've flagged this internally and will investigate! Thanks for your patience!