We had a three resort stay during our recent trip: 1 night All Star Movies (purchased our mug), 4 nights Old Key West (used our mug) and 6 nights Tree House Villas (hardly used our mugs but they worked).
We did not have any problem using the length of stay option.
In your circumstances, I suspect that you may have a problem. It sounds like you have a stay with the meal plan, two nights no meal plan, and a stay with the meal plan. It is my understanding that you will get two sets of mugs. good for their respective stays.
The mugs sold for length of stay, are good for about three weeks! So if you get a length of stay with each set of mugs, you won't have a problem, but if you are only staying for one or two nights, you may have a problem depending on how the mugs are coded.
Hope that's a help.