What's probably going on is a difference in acceleration and jerk settings between the slicer and the machine's firmware. The print head doesn't move at a constant rate, the speed that you tell it to print at is actually just the maximum 'speed limit'. Acceleration is exactly what it sounds like, and jerk is the instantaneous speed change that's allowable, instantly jumping from 0 to 40mm/s for example... The slicer will assume a value for both of these settings when it calculates the printing time, but how your printer handles the GCode can vary based on the firmware that you have loaded. I'd bet money that this is what's mismatched, and causing the discrepancy.
For example, the slicer may tell the print head to speed up to 60 in 1 second, but if your firmware's jerk is 40 and accel is 10, it would actually take 2 seconds to reach 60 (40 instantly, plus 2 seconds of acceleration). Do that times a couple hundred infill and perimeter lines, and you're off by several minutes.