When inputs from Factory I/O don’t work you probably need to make sure the input addresses used by Factory I/O are not shared with physical inputs.
Input signals with intermittent / blinking behavior is usually caused by interference between physical inputs of the PLC with inputs from Factory I/O sharing the same address. Values transmitted by Factory I/O are being overwritten by the values of the I/O modules as their state is copied to the CPU process image, which will cause blinking/the impression that inputs from Factory I/O don’t work.
You can solve this in two ways:
Use different addresses
You can either use different input addresses in Factory I/O by changing the Offset in the driver configuration window:
Or change the addresses used by input modules, leaving addresses near 0 free to be used by Factory I/O:
Set the module PI to none
You should do this for every input module of the PLC, either digital or analog.
You can also refer to step-by-step guides on how to connect Factory I/O to various Siemens PLCs.