I could have the French Onion soup in the MDR every day, no problems. Have it at Cagney's or Le Bistro and I have some digestive issues, worse at Le Bistro. So, yes, there IS a difference. Maybe it's a different cheese? I think some mass-production kitchens will use Swiss or a cheaper cheese on top, while traditionally I think it'll have Gruyere so maybe it's that cheese I have an issue with.
No, the issues are not onset of Norovirus, it lasts one round and then done, and it's happened on multiple cruises after having that soup at those specialty venues.