There are two separate issues.
1. How HyperSizer analyzes the spar caps for strength, buckling, etc.
2. How the FEA returns loads based on the FEM configuration (stiffnesses and offsets)
1st Issue - Spar Cap Analysis in HyperSizer
The spar caps are either bonded or bolted to the skin of the wing box so it is diffcult to quantify an accurate buckling mode for these structural components. They really should not be treated as simply supported beams since the skin is providing some buckling stability. A local buckling analysis with Simple-Free BC would also be very conservative. My suggestion is to deactivate all beam buckling and local buckling analysis methods for the spar cap beam components. This leaves material strength as the controlling failure method. To analyze spar caps for strength, use the "Cap Beam" concept in HyperSizer.
2nd Issue - Accuracy with FEA.
Resolving the second issue is a matter figuring out the best way to offset the CBAR elements so the FEA loads are accurate. If you are using CROD elements, there is no offset, so this does not apply. For cap beams, the offsets on the options tab are putting the grids at either the top or bottom of the cap beam. They are not moving the beam left or right. For the forward and rear spars, to ensure the offsets are putting the bar elements at the correct place so the C-beam spars can be modeled, I would suggest using an L-beam for the caps. Just set the height of the beam to the thickness of the lower flange + 0.001 (see attached image). This way the offset selections on the options tab will move the elements so that the grids are represented at the corner of the cap. Be sure that the beam +Z (HyperSizer), is pointed out of the box structure, so it is consistent with the image on the concepts tab. This approach should not be used for sizing, rather for updating the FEM with the CBAR offsets and beam stiffnesses.
Let me know if this is not clear.
-James