MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Well 400 or 1000mm/min do not say much without more information (at least about the pulley diameter and gear ratio if any or steps per milimeter). How many turns per minute of output shaft is it? If the motor is doing 15RPM at 400mm/min, than you are already hitting the limit there.
Vref 0.15V is again not enough to judge. What drivers are you using (A4988, DRV8825, or other), what are the sensing resistors on it? Please follow webpage: http://reprap.org/wiki/Pololu_stepper_driver_board rather than a recommendation for some specific situation.
Firmwares on Arduino boards are usually highly optimised as 8bit hardware lacks computing power and for that reason prone to error under specific situation. From what I have tested, Mega 2560 with DRV8825 can do hardly more than 9000 microsteps per second and axis reliably. You can get a bit more from A4988, not by much though. But G6 and SEGMENTS_PER_SECOND have no firmware I am familiar with. That is probably some speciality of Hangprinter so it is hard to say if these limits are working there as well.
If (judging by the name) SEGMENTS_PER_SECOND will give you lower resolution hence less calculations per second that your problem is definitely in computing power.
You are welcome, but actually I am not very helpful as this type of printer is strange to me.