While the anomeric effect can cause stabilization of molecules, it does have a magnitude to its stabilization, and this value can be overcome by other, more destabilizing effects in some cases.
In the example of spiroketals, the orientation on the upper left shows stabilization by the hyperconjugative anomeric effect twice, thus greatly stabilizing the orientation of the molecule. The orientation on the upper right only shows this hyperconjugative anomeric stabilization once, causing it to be the lesser preferred structure. However, when substituent are added onto the spiroketal backbone, the more preferred structure can be changed. When a large substituent is added to the spiroketal backbone, as seen in the lower left, the strain from having this large substituent, R, in the axial position is greatly destabilizing to the molecule. In the molecule on the lower right, R is now in the equatorial position, which no longer causes destabilization on the molecule. Therefore, without substituents, the upper equilibrium reaction is favored on the left hand side, while the lower equilibrium is favored on the right hand side, simply from the addition of a large, destabilizing substituent.