Had the Same issue, this worked for me
Backup all your Important Data (just in case)
Disable Auto-Brightness and Energy-Save Option.
Play until your Battery is low and your 3DS isnt Starting anymore.
Take out the SD Card with Emunand
Take out the Battery for 5 Hrs+ (Better over Night)
Put the Battery back in and overcharge it
Fire up your 3DS (without an Inserted so card) and Format on Sysnand (be aware) this unlinks the Emunand from Sysnand !
And now try if the flickering is gone.
Overcharge in Detail:
Play your Battery down until the device isnt Starting anymore
Charge the Battery back until it is fully loaded (the light goes out but LEAVE THE POWER CABLE INSIDE THE DEVICE, SO IT GETS CHARGED EVEN YOU DONT SEE IT - Better over Night)
After 2+hrs in this State (or After you Wake up), unplug the Power cable and Plug it back in.
And leave the device in this State for 2hrs+
That is an overcharge.
Every Device nowadays notices if its fully charged but even this, needs to be calibrated.
Charge your Device once or twice in a month with this Method and you will notice an Huge Gain in Battery life and Play Time
Little Tip:
After buying a new electronical Device i charge it this way the first 4 Times.
Then only once or twice in month this way
Every of my batterys work like new, from iPhone, over PSVita to 3DS