After some more reading i tried to do the folowing:
rewire the pins MS1-MS3 so that i have a connection from 3 OUTPUT pins on my chipkit and reading 3buttons and if i read HIGH on the button (pressed) then use digitalWrite(MSpin, HIGH) and if the button is not pressed then i write LOW. (with no resistors this time)
and as wierd as this sounds, i can only get the motor running in full step or quarter step.
only the button connected to pin MS2 has the desired effect.
I've checked the button wiring and as debug i output the values of buttons pressed or not and the buttons are fine.
as for the current limiting, my thought proces went in a way that i should keep the current lower since the voltage is higher and keep the power in balance, example...
i have a motor rated 3,9V and 0.6A P=U*I gives me 2,34W in order to have the same power with 12V the current should be 195mA and 70% of this is 136mA (and i thought that that is the value i should read from my ammeter.
i use this boards: pololu.com/catalog/product/1182 so i don't have a ref pin i can access but i tried to set up the current higher (for the motor with 3,9V and 0,6A that would be 0,42A) and the motor gets rather warm, is that normal?
EDIT: things just went from wierd to bizzare... i went checking if i might have made some errors while soldering and if there is a short circut somewhere or some other abnormality, didn't find anything, but as i gave it another go, the damn thing started to work (i also tried it with another A4988 driver and it worked fine, and then with the first one again and it worked as well)
when things are not working and you don't know why its strange, but when they suddenly start to work for no apparent reason its even worse (cause i'm afraid they will stop again).
Another question/idea. Could it by any chance be that the problem comes from me not using any capacitors on the vcc and vmot lines? considering the power suply comes from an atx power supply that should be relatively stable (and im guessing the same about the chipkit's 3.3V line)?