One of my friends had a Giant that cracked along the seat tube as well. To weld aluminum, the area has to be cleaned of all paint and oxidization (that white powdery stuff that forms on aluminum). Afterwards, you pre-heat with a torch, complete your weld, and hit it with the torch again. By torching the area, it helps the area to cool more slowly, which lessens the chance of a crack in the weld.

If its still got a warranty, take it back! You might find that scoring or slotting the area where the crack originally occurred could help but thats a bit more risky than welding (in my opinion) Its easier to remove a weld and score something than to notch the area and then have to reform it.