Extenuating circumstances like Pig Flu are treated differently. A number of cruises violated the "Jones act" - there was no choice. I don't know of any being fined.
The same has been true of cruises affected by inclement weather and missing ports.
There are different requirements depending on if a foreign flagged cruise ship embarks and disembarks in the same US port vs two different US ports.
I don't think Congress cares about the law - however at least one union does.