My bending moments are far less than beam theory calculations

Check your material properties. Do not use undrained material for 2D elements representing the beam. Or insure that fluid bulk modulus for such elements, Kw=0. BM is calculated from effective stresses and setting Kw to a large value implies having an undrained material. This will produce reduced effective stresses, hence erroneous bending moments.

I have selected a series of adjoining elements but when I try and generate bending moment plots/graphs, I get the message 'Selected elements must be joined, please reselect elements'

Try selecting the elements in sequence so that each element that you select is adjacent to the previous one or go to Select, Order Selection and then choose X or Y as appropriate.
If this doesn't work, your SCD file has become corrupted, probably by deletion of elements. The file should be emailed to SAGE for hand modifications