Are you saving your vi structure in a llb before building it up? If you do it this way, make sure you include dinamically loaded vi's, at least in LV 5 they are not included unless you do it manually.
If this is not the problem i have really no idea, i would try reinstallyng application builder.
Good luck
P.S. Don't worry for the one star rating, nobody is going to give me anything for collecting stars... i'm pleased if i can help