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Replace U1900 and see if it fixes the problem VRTC should be 3.3 steady.
If it does not, next places to check would be U1950 pin 8, the SPI ROM traces and termination resistors and the JTAG. But you need to steady out the clock voltage first
I don't have a spare clock chip but I'm not sure that the rtc is not ok . Pin 8 on u1950 is pp3v42 which is stable. I will check the spi bus but again - this feels like a different kind of issue on the S5 5v regulator circuit. Like a diode failing as a cap discharges perhaps.