What printer are you using? Most of the prints I do have very accurate estimates within a few minutes of the multi-hour build time, but you may need to calibrate the results if you're using a homebuilt printer or one where you modified the acceleration values in the firmware.
To calibrate the settings that S3D uses for the time estimates, go to Edit Process Settings > Speeds tab, and look at the "Time Estimation" section in the bottom left. Make sure to set the XY acceleration and jerk to match your printer firmware.