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@Gordon
The initial pause a few seconds after power-on is to be expected I'm afraid. I believe it's a side effect of the way the Pico has to handle timing - the RTC is only 32kHz so to get timing accurate to more than that that also follows the RTC, it has to 'follow' the RTC time with a high-res timer, and it takes a while to keep in sync.
It doesn't pause when connected to the computer because it doesn't attempt to enter any kind of sleep mode when it has an active USB connection.
However, I've just set up something to detect if LED pulses are out of range and I haven't got any long pulses in over 30 minutes. Is it possible that something could be causing the Pico to restart, which is causing the repeated pause?
To avoid that initial pause, could you wait for a few seconds after boot before starting what you need?
Also, I know you say this is part of a bigger project (thanks for narrowing it down!) so you may be doing more complex stuff but if you do need a pin to be pulsed at an accurate interval then you could use the PWM hardware with
analogWrite.