To be honest, I haven't tried Proteus and PWM, I do have a piece of software that drives LED's from a transistor, FET i believe I used in the end, so I could try and dig it out and see the results.
I used this to sink and source the LED's to a 12v power supply.
I haven't found anything else that closely matches what Proteus can do though, if someone knows of something better than Proteus for simulating a real world circuit then i'm all ears!
I will check in work as I dont have a personal license for Proteus, but I'm sure a colleague of mine has used Proteus to simulate a PWM circuit.
Wilksey