The requirement for a pull up/down resistor depends upon the characteristics of the signal source.
If the signal is supplying proper zero and one voltages, and switching times within specifications, then a resistor is not required. Too much time in the forbidden zone, between one and zero, will cause issues such as you are seeing.
But, for a definitive answer, you would have to tell us how the signal is being produced.
The PowerStep01 stepper drivers are producing the signal; Active Low. Are we thinking that they are constantly toggling the Flag pin? I’d have to break out the scope to find out (sigh).
EDIT: The datasheet says its a latch and does not toggle continuously.
Chat GPT says that TinyCLR is internally polling the signal and producing the interrupts. Is that true? It could save me from having to pull out the scope.