I tried using ACLS, CLS, and GCLS to fix my problem, yet the screen still keeps on blinking! What else could be the problem?!

Could you tell me blinking frequency? (once a second, or faster?) Or, there is a possibility that the automatic brightness adaptation for low power consumption will malfunction. Do you use your 3DS with ac adaptor?

Do you have any wait time in-between clears longer than 1? Show us your code.

Take ACLS, CLS, or GCLS out of your loop.

You do have a WAIT or VSYNC within your loop, right?