Having trouble controlling 3 Row Seven Segment with 4 shift register 74hc595

Was that powering the display directly when it was flickering? The display does not seem to have its own voltage regulator. 9V could have fried it. Or did you power the Arduino with that PSU and then power the display from the 5V pin on the Arduino? The Arduino's regulator may have been overloaded.

And you are powering the Arduino and display from USB power now?