Not really sure what's different about this png, but GIMP says it is 'Greyscale' and WebStorm says it is 16-bit, but it shift it's color (they become lighter) in resulting sprite.
Attached is a test case, which shows difference clearly. There are couple other files with similar properties with the same behavior, let me know if you need them for further investigation.
Sorry if this is known issue. Thanks for great tool!