I hope someone finds this useful.
OK, this is working: I repeated the command, first with 1 step and then the full 1000 steps. Now, the motors move together in the same direction.

```
digitalWrite(X_DIR_PIN, HIGH);
simpleAccel(1);
digitalWrite(X_DIR_PIN, HIGH);
simpleAccel(1000);
digitalWrite(X1_DIR_PIN, HIGH);
simpleAccel(1);
digitalWrite(X1_DIR_PIN, HIGH);
simpleAccel(1000);
```

GitHub: [d333gs/Code update](https://gist.github.com/d333gs/6f017ae1f41bfbc67eedb23ee1991c0c)