I've found out the parts I've printed will contain too much filament. Outside dimensions are greater than should and all holes are smaller. I've used Cura and Slic3er and the problem seems to be the same with both software.
What could be the reason the filament flow have to be set to 85-90% to get correct result in Cura? I haven't make any test prints with Slic3r to fix this issue.
I'm using the machine which is designed by Reprappro and there is Melzi electronics. Should something to be changed in the firmware? I'm using 1.75mm filament and check measuring of the diameter confirms the size is very accurately 1.75mm.