Probably not! Most warrantys are useless. for example, I once saw a warranty that stated, shingle blow off would not be covered if the wind blew over 15 mph.
Barb may be able to take the builder to court if they are still around. With the right photos, she could probably get a judge to rule that reasonable industry standards have not been applied in the construction of building.
If this is the case, bring estimates from three longstanding contractors to repair the work. Do not agree to have the first contractor come back to do the repairs. (If they did not know enough to do it right the first time, they don't stand a chance the second time.)
It sounds to me, without seeing photos,(you can send them if you would like), that this is a three walled, porch style, deck. If this is the case you will probably need to add scuppers. I would add an opening not greater than 4 inches in height,(for code reasons), and at floor level if not, less than floor level, so any water would not be able to build up.
Also I would re-do all the flashing. Don't forget to replace all the insulation. Wet insulation will mold and mildew. Check any electrical boxes for moisture as well.
Do you have a step down from the door to the deck? Is there a rubber roof under the decking?