I've ran jobs over 3 hours many times, and the longest was over 7 hours. The laser should have sufficient heat sink and cooling to maintain temperature within its operating range.
Benbox doesn't allow you to change resolution, so you will find all jobs take forever. In many cases you need a lower resolution to prevent burning or "blurring" of the image, or just because you want a quicker result and can sacrifice some quality.
@nottingham82 why don't you reverse the axis in T2Laser, or as you said, swap the Y-axis cables?