To change microstep mode, normally there is a jumper or solder bridge. I looked at melzi page and it appears to have solder bridges from MS1&MS2 to 5v. If you check datasheet for a4982 chip, it will say which combination of ms1&ms2 corresponds to each microstep mode. Yes the movement being slower could be related to other things than driver or motor indeed even a firmware setting or even z endstop issues.
You can try set the vref higher, its not that you have to specifically avoid that. What i was saying is only that it is probably pointless. The driver watches the natural current growth in the coil and interrupts it when it gets past the mark, but your supply is 12v and coil is 30ohms, so it can never go past 0.4a, even if the driver is waiting it to get to 0.8a for example, if you want to have a setting like that then it wont make a difference because it cant reach that mark.
You can try set the vref higher, its not that you have to specifically avoid that. What i was saying is only that it is probably pointless. The driver watches the natural current growth in the coil and interrupts it when it gets past the mark, but your supply is 12v and coil is 30ohms, so it can never go past 0.4a, even if the driver is waiting it to get to 0.8a for example, if you want to have a setting like that then it wont make a difference because it cant reach that mark.