Just to clarify something, you say 03 CR250 which should be case reed induction - maybe some pictures might help. I have encountered this problem myself and cracked cylinder base flanges are very difficult to repair. The two methods of welding possible are TIG and MIG. With TIG does the welder have sufficient room for the torch to access the crack? It might be better to use MIG to do the repair.
It is critical with aluminum that the area to be welded is as clean as possible - two stroke mix residue will screw up any weld.Make sure that a proper weld prep is done,don't worry about cosmetics, and make sure that ALL of the crack is accessible. Make sure that both a pre heat and post heat are done and that the welding may have to be done in stages to prevent cylinder distortion.
Don't be afraid to lay on the material - this is the only way the weld will hold.I suspect the welder did a single (cosmetic) pass with a tig torch and as such will never work.
I once had to repair an IT200 cylinder that had suffered through a number of previous failed attempts. I layed on the weld almost a 1/2" (13 mm) thick and it looked ugly as hell but the repair held. IT200 cylinders are almost unobtainable.