I reailsed that too, but have no idea what's the reason. A wild guess would be that pronterface simply takes the remaining steps divided by the time taken for the last step to estimate the remaining time. Because it processes the information line by line, it's not able to foresee what's ahead, and there are lots of paths with varying speed. Hence, the difference. Again, this is just my wild guess.
I'm using kisslicer, and the estimated time by the slicer is usually pretty accurate.