With a MICROFLEX (using the case as the negative path), you can wire it either way because the negative path on the driver is continuous in the driver.
With the MICROBOOST you must use the case pin to negative driver input wire technique to use the case as the negative path. The negative path in the microboost is NOT continuous. If you bridge the case pin to the negative pin, when using the case as the negative path, you effectively bypass the driver (giving the diode a direct connection to the battery).
@ the OP -- Check to make sure that you have good electrical connection at all contact points. The possibility of an anodized contact point may be it. Also, you may have a short or a break somewhere that only manifests itself when it is assembled. Finally, make sure that you are placing the battery in the correct direction and that it is actually making contact at both ends.
Peace,
dave