Doing what you described sounds like you put a whole lot of gas into the bottle, and it didn't have a chance to dissolve into the liquid. Surface area of the liquid vs surface area of the gas are big factors in how quickly it will dissolve. If the gas was not bubbling through the liquid because it was only a half bottle and the gas injector was shooting into the airspace and not the liquid, the surface area is only the area of the disc of liquid at the top of the column made by the bottle. If the gas bubbles through the liquid, it forms spheres, lots of spheres with a massively greater surface area contacting the liquid. If the liquid was warm... or not as cold as possible to make it, the amount of gas that could be dissolved is lessened...
So, for an appliance that does not allow you to do stuff that could encourage gas dissolution in sub-optimal circumstances (like chilling it for a long time before opening the bottle, and shaking the hell out of it), you have to just follow the directions.