Using an Arduino Mega GPIO pin to enable MAX1771 DC/DC converter
Firstly the shut down operation - the MAX1771 is a boost converter and when "off", the MOSFET is also off and so the incoming voltage is transferred through to the output via the inductor and 1N5819 diode. So you will see a little less than the incoming supply at the output. It's not a shutdown feature as you expect - i.e. it doesn't turn the output off; it just turns the chip off.

Regarding the failure to boost (given that it once did), either you have wired the new circuit up incorrectly or you have unwittingly destroyed the chip or MOSFET.