I read your posts again and there is a lot of problems:
I am using the pwm from the atmega, the default 976hz is too small I would like 7812hz or 62500hz
Flickering at frequency of 100Hz or more is no more visible by human eyes.
What probably happens, is that PWM frequency and 100Hz of the rectified mains voltage are not sincronized and the beating of the two frequencies is producing low frequency flickering. (like aliasing in DSO)
The only solutions are feeding the led strip with filtered DC or use a phase control at 100Hz.
I use a rectifier bridge so the led strip is powered with DC
Can you do that ? It is a 220Vac led strip, what is the internal schematic of this strip ?
If you have a resistor in serie with two led's in anti-parallel, feeding with DC instead of AC, you will have only one of the two LED's working and he will have to much current (two times the nominal average current)
It was intended for AC and, in my opinion, you can't feed it with rectified AC voltage.
...is intended for use at probably under 10% that is why all the dimming and pwm needs.
Can't you feed it with a lower voltage ? 110Vac for exemple ? You could use a 110Vac dimmer.
...and that is a really nice chip (LM3445)
This chip can be used only with LED's without current limiting resistors. Can't be used with your led strip.
...but I need to control the dimmer via software.
Easy to do with a modified dimmer and an optocoupler 4N25.