LCD Display Flicker When Arduino Main Board Supply Voltage to GSM Shield Board
This sounds like either your GSM Shield is drawing to much power (from time to time) and thus your Vin drops resulting in flickering or your GSM Shield induces ripple on top of your Vin.

To debug this I would recommed to have a look at Vin with an oscilloscope and see how stable Vin is. Additionally some capacitors between Vin and GND (100nF and 10-100µF) and a ferrit between Vin and the GSM Shields Vin might help.