Ok here's what I have analysed so far. The capacitor does not do anything more to my circuit. so with it it still doesn't work but I will keep it there since it doesn't hurt.
I am using two different sources from the university, one is outputing 9V to a LM7805 (5 Volt regulator) which goes to the Microcontroler. And that source is rated for 1A of current, which is well enough for the MCU since it only takes about 30 mA when running.
For the H-Bridge part, I am using a Source of 4.4V (Outputs exactly 3V to the motor) and this Source is rated for 2A, which is the Stall current of my motors and i've never seen them taking more than 700mA.
So both sources are seperate and both grounds are connected together.
When I try to run with the PWMs from the motor, the MCU will reset on its own( I know because on startup it goes in a Stop Loop which waits for me to press a button before I can send a signal and After I try to run it it goes back to that loop).
Now i tried puting out VCC to one side of the bridge and Ground to the other side. well that worked PERFECTLY.
So to sum up, the problem relies on that MCU, My h-bridge is supposely demanding too much current from the MCU and it crashes. I have 1K resisitors with a voltage of 5V to the gates. so that means the h-Bridge shoul only demand a maximum of 20mA and the MCU can handle over 100mA.
Any more Ideas?
Thanks
Marc