Hello,
Recently while doing some fluid simulations, normally if I bring in an OBJ mesh file into Blender to use as the fluid obstacle, it doesn’t work, but if I use a mesh I made in Blender for the fluid sim, it will normally work.
Any ideas as to what this could be? I’m thinking it maybe just be 2.5, so I’ll check 2.49 soon as well. 
I have used obstacles in 2.49 with a fluid system. What you have to remember about bringing in OBJ or any file is that the importers will sometimes create duplicate veritices on import. So the general work flow is to import the OBJ. Put the OBJ into edit mode. Remove doubles. Then do a SHIFT-J to convert as many triangles into quads as possible. Also a recalculate normals outside after a remove doubles is a good idea too.
Try the OBJ fixup and it may work with your simulation.