Boost converter, once enabled, can't be disabled
It sounds like you have a connection between the boost converter's Vout pin and the Enable pin.  If so, the converter's output is driving its own Enable pin high.  This is collaborated by the comment you attached to your question.  Perhaps your pullup resistor is in the wrong place?

In any case, the Arduino output pin may get damaged by the overvoltage condition.  It sounds like it's still working (so far), but something to keep in mind.