Microstep Select (MSx). The microstep resolution is set by the voltage on logic inputs MSx, as shown in table 1. The MS1 and MS3 pins have a 100 kΩ pull-down resistance, and the MS2 pin has a 50 kΩ pull-down resistance.
Are you using a bare Allegro A4988 microchip, or are you using an A4988 module such as those sold by Pololu?If it's the bare microchip then this is an extract from the Allegro A4988 datasheet that I havewhich suggests that your jumpers need to pull the pins HIGH....R
The chip has only weak pull-downs, so if there is any length of trace from the MSx pins, add external 4k7 pull-downs as well to avoid noise-pickup.
If it needs external pull downs, much stronger ones would be better. Depends on trace lengths.