That isn't a case of bad batteries and buying more won't cure the Stubby problem, it is caused by bad electrical circuit connections and/or using materials that don't have particularly good conductivity. With the Stubby/Empire mod the wires are held in place with a screw instead of being soldered in position. If a wire is soldered it will give a solid connection and, as the connection is enclosed in solder, no juice/contaminants are likely to interfere with the connection so it will it will probably stay good. In the case of the Stubby/Empire mod the wires aren't soldered to the board but are held in place with screws - crap SHOULDN'T get in to interfere with the connection - and the screws SHOULD stay firmly in position but obviously sometimes it does. Personally, instead of tightening the screws as recommended, I would remove the screws and the board and spray both with some electrical circuit board cleaner to make absolutely sure the board connection points, the wire connectors the screws go through and the screws are clean and dry before reassembling. If juice or contaminants are present tightening the screws may press the connections more firmly in place but the crud causing the problems won't necessarily be removed so the problem is more likely to return.
The reason the board is cutting out early/giving low power warnings when the battery is still at half charge is directly related to bad connection problems. Bad connections in a circuit cause resistance and heat build up inside the mod itself - this drains power. When a mod is idle the board will not be pulling much energy from the battery, just enough to read the resistance of the coil, the battery level and operate the screen - next to bugger all, so - even though there will be some drop in current through the bad connection it will be a fraction of bugger all so the screen display will still show a half charged battery. When you press the fire button this changes as the board will be trying to pull a lot of current from the battery, - a lot of current going through a bad connection generates heat and consumes more energy so you can end up with a situation where the battery is at say 3.75V but only 3.2V manages to actually get to the board - the board detects the battery is low and displays a low power warning even though the battery still has plenty of power. it is also why the same battery will continue to run in another mod when the Stubby/Empire has refused to fire.
Obviously not everyone will have this issue with the mod but the fact Bogan made a vid telling people to tighten screws to get a better connection means it has happened to enough people to be a known issue.