Interesting. I'd have to run the math to check it but I think the problem you were having here was the 1K resistor. The transistor might not have been at saturation and so the gain may have been too low for amplifying the PWM. I'm surprised it didn't work. I use the same circuit to control the fans on my tank.
Good call on the pull-down resistor. I always surprised people neglect them, not just for safety but also to just have a nice product. Why would you want you LEDs going to 100% any time you unplug something?
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