all leds illuminate. the flickering led flickers but the others do not
Do you know if the LEDs are getting any PWM signal, or are the on because Q1 and/or Q2 are saturated?
Instant analysis based on very little information . . .
Because Q2 is supposed to operate as a saturated switch, a very small minimum continuous current through D6 will keep it on all the time. And there must be a small continuous current through D6 to power the flicker control circuit. Q2 amplifies that small current by 100x, and pushes that through R2.
Let's say it takes 2 V Vgs for FET Q2 to sink enough current for the main LEDs to come on. That is a minimum current through R10 of 200 uA, and that is a base current into Q1 of 2 uA. So, if the minimum continuous current through D6 is high enough that even through a lot of it comes through R1, at least 2 uA comes through R3, the main LEDs will be on.
Something else to consider -
D6 has a minimum operating voltage requirement, below which it is off all the time. And Q2 has a minimum Vbe of around 0.5 V for any useful collector current. When running on 3 V, this leaves a small range of voltage across R3 for circuit operation, but that range is a significant percentage of Vcc. As D6 goes on and off, the voltage across it goes up and down, modulating the current through R3 up an down around the 2 uA trip point for the output changing state.
Change Vcc to 12 V, and everything changes. The ratio between the voltage drop range across R3 for operation and Vcc is now probably 10x what it was at 3 V. Because that operating voltage range now is such a small percentage of Vcc, finding the R1-R2-R3 sweet spot for circuit operation will take some tweaking.
Starting point - replace R1 with a 100K pot, and see if any value of R1 will work with R2 and R3 at 10K. A scope across R1 will tell us lots.
ak