The stock battery percentage will actually read 100% kinda early.. (found this out by testing 2x battery app)
I noticed the phone shows 100% but 2x was only 96%. So once its reaches 100 let it stay for another half hour or so, to reach MAXXimum capacity.
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This is very close to what BatteryUniversity says. Based on their description, since Lithium Ion batteries can not accept a continuous trickle charge once they've reached their maximum voltage - usually set at about 4.2V (which applies to Lithium Ion Polymer batteries as well), the charging circuitry is designed to shut charging off completely to prevent an overcharge and shorten the life of the battery as well as to reduce the risk of even worse consequences such as overheating and possible self-destruction (catastrophic failure). This is evidenced by the fact that the lightning bolt on the battery will disappear once the battery has reached a full charge.
Once that charge level is reached, the stock meter will show 100%. Now, what happens from here is where it gets interesting. If the phone is OFF, in all liklihood the next time you power it up, it'll still have nearly 100%, if not 100% charge. However if you are like most people, you will charge the phone while it's powered on. This is what leads to incorrect meter readings, and incomplete charging cycles. Since the phone will be drawing current and may actually have some services running that will do such things as check email, sync your Facebook and LinkedIn accounts, etc., even while you are sleeping, it will be drawing current at varying rates.
The charging circuitry is looking for two things to happen that signify it has reached nearly a 100% charge. First it's looking for the voltage to level out at 4.2V (or very close to that for most LI/LIPO batteries). Then as it's approaching a full charge the current draw by the battery will exhibit a signature drop in the rate of current it's pulling. This is when the charging circuit says..."The battery is almost full and I need to reduce the charging rate to top off and once done, interrupt the charging completely). It then charges at a much lower rate for the last few percent of charge until it shuts down the charging circuitry.
If the phone happens to pull power and make it look like the battery has been pulling more in the charge process, and then the phone suddenly stops pulling so much (like immediately after an email or Facebook update for instance), the charging circuitry could mistake that sudden drop in current draw for the signature that normally identifies the battery is essentially full. This could cause the charger to shut down far too soon and leave you with a battery that is only charged as much as perhaps 80-90%, however the meter will incorrectly display 100% until it has had enough time to adjust for the increased consumption once the phone is being used. This is one reason why many people complain their battery apparently "drops" 10% within minutes of being removed from the charger. Truth is, it was not full to begin with but the meter believed it was.
The second possibility is that it did manage to fully charge, and then the charging circuitry shuts down. Now the phone is using power but the battery is not being replenished until it decreases to about 90% of full, at which time the charging circuitry kicks in again and boosts it back to 100%. This is done to protect and extend the life of the battery, since studies show the longer the battery is held at 4.2 volts the shorter its lifespan overall. So by letting it hit 4.2V, but then shutting down charging and allowing it to decrease slowly to maybe 4.05V, it extends the battery's life and only reduces the available charge by no more than 10% at any given time. So if you pull it off at 92%, but it shows 100%, then you use it for 5 or 10 minutes (using about 2%), it seems as though it's suddenly "dropped by 10% in less than 10 minutes"!
This top-off to 100% and slow discharge to 90% cycle can happen several times over the course of a night's sleep. During this time, the meter will continue to show 100%, since it only moves in 10% increments. So when you pick it up and unplug it, you think you have 100%, BUT may only actually have 92%, and the other 8% was used up by the phone during the last period of no-charging. This relates to your example above. But in your example where the phone said 100% and 2X showed 96%, leaving it on for an additional half hour may actually allow it to continue to deplete the most recent top-off cycle and by the time the half-hour has passed not only is it not 100%, but could be 91%! Unless you happen to remove it right at the end of a top-off cycle, you will not be assured a 100% charge.
In that situation, it will not begin the top-off charging again until it reaches 90%, so if you pulled off at 92%, or 2% too early, the result is you have 92% of the battery's capacity in charge for the day. The only ways to assure you have 100% charge are to either charge with the phone powered off, or monitor its charging process and when it reaches 100%, remove it from the charger immediately.
