Never had a problem with WinISD and round ports. They've all come in as expected, or within the small tolerance that the human ear can't tell the difference.
Did have a problem getting a shelf port to act right though. As I understand it, there is a bit of the cabinet walls acting as a port "lengthener" when the port is particularly short in height compared to it's width, or maybe just shelf ports that don't have much height in general.
Some discussion of it in this thread. Cab building question about shelf port length...
This online calculator http://www.carstereo.com/help/Articles.cfm?id=31
is said to be more accurate with the shelf ports.
Ironically, when doing some preliminary modeling on my next build, the car audio calculator and WinISD both gave me the same length for some 2" x 5" shelf ports. The car audio calculator will not accept measurements that have a height to width ratio of greater than 1 to 8. WinISD will. Perhaps that has something to do with the inaccuracies?
Never done a really detailed build thread here. The next one (if I can ever get damn time to do it), I will take photos, do some step-by-step and explanations. Will include final measurements vs. modeling program predictions, etc. Don't expect it anytime soon though. Ah...life gets in the way sometimes....such is life.