LEDs are not glowing with same intensity in LED matrix
74HC595 is a poor chip choice, able to source just 70mA total for all outputs before being overstressed.
You will see more consistent results with a proper hardware setup: Two MAX7219s, one for each display, outputs multipexed at 800 Hz, simple register write to update a column or row;  or if you insist on implementing your own multiplexing, then MIC5891 for current source to the anodes and TPIC6B595 for current sink on the cathodes.