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Hi Iņigo,
I think it has to do with the idle/suspend behaviour. After 5 seconds of idle behaviour (I.e. no 'busy background' and no windows-events for 5 seconds) a suspend mode is triggered, which stops the cpu-clock (as far as I understand the code/script correctly). I assume that the cpu wakes up from this when a button is pressed, stylus is used, battery is empty, usb is connected, ... These are all 'externally' triggered events that (presumably) trigger an interrupt to wake-up the CPU (i.e. start cpu-clock). The purpose of this all is to limit power consumption. The downside is that the timers like you use them will not fire until an external event occurs.
Can you try to set the timeout to smaller then 5 seconds? That would 'confirm' my ideas on the internal workings of the firmware/hardware.
You already told that the clock is not even updated when you turn-pages, that would contradict with my idea above...
As another experiment you could show mm:ss instead of hh:mm and update every second, 2s, 5s, 10s, 30s to see if you get updates at all.
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