There is no difference where the configuration comes from, the spectrum can be computed for any structure.
The difference between graphene (I assume you mean from the Database) and the sheet (assumed from Custom Builder) is perhaps in k-points; the sheet is a supercell, and if you have too few k-points, there results will differ, but will be the same in the limit of infinitely many k-points. For infinite graphene it is usual that you need many (really many!) k-points to get converged results.
