From my understanding, the beam system used for concrete beams is based on the footing family. ie the developers just took this family and modified it slightly, but put quite simply it doesn't always behave nicely.
I have created a new family that seems to work well, although it does occasionally misbehave, it works alot more reliably than the OOTB family.
Structural Framing Family (with the following settings)
Always vertical
Symbolic rep: from family
Structural material type: (pick your poison, but mine is set as precast)
Display in hidden views: Edges hidden by other members
show family precut in plan
I also leave the start and end extrusions in the parameters, because this allows me to manipulate the ends of the beam when it doesnt play nicely. Usually if I drag the grip back, so its not past the centre of the adjoining beam, then join geometry, it works just fine. Also looks nice in section and joins (assuming materials are the same) with floor slabs well. Another neat ability is that this family can 'cut geometry' so you can cut it at the face of shore walls for example rather than having that ugly soffit line at the wall faces. The OOTB family, being based on the footing family, can not be 'cut geometry'
Adrian, one of your melbourne counterparts will have a copy of this family as I sent it to them to try out, sorry but I dont have the family available with me to link it here.