There seems to be a small number of modules that actually use the "opposite beam exists" checkbox, however most don't seem to be impacted by it.
For connections that don't use it, the option should either be removed, or the module should be updated to account for the opposite beam. Currently you could put a shear load of 1 billion kips into the box for the opposite beam, and it would tell you everything is fine.
There are cases, for example columns with beams framing in on both sides, where it would be nice to be able to design both connections in the same module. It seems like someone started to add this feature with the "opposite beam exists" checkbox, but it was never finished
If you can add load on the opposite beam and nothing happens, it sounds like a problem.
For those interested, see AISC 14th, J10.6 for Web Panel Zone Shear; see the commentary for the same. The commentary provides figure C-J10.3 for beam loads on a column, and formulae to evaluate the loads applicable to design of web panel stiffeners, i.e. web doubler plates and diagonal stiffeners.