Tested your craft file. Your top radial orange tanks are not attached to the Girder like you would expect. I imagine that something went wrong with symmetry, either you attached the bottom tanks to the central tank first, or KSP decided to redo the connections. Either way, take the outer tanks off, attach the upper tanks first, then attach the lower tanks and strut them to the central tank. You are not going to be able to use the girder for the lower stage as KSP does not allow for more than one attach point(besides the strut).