If one is prepared for a Magical Weapon strike or an Area Effect blast, one may be able to seek cover and gain the bonuses listed above. Similarly, being caught off guard with either of these two types of Saving Throws will result in penalties to the Saving Throw. It is much harder to dodge a Magical Weapon energy ray or survive an Area Effect explosion if one has no idea that they are about to happen. The penalty to the Saving Throw for being caught off guard for these two Saving Throws is -2. This generally applies to the Surprise Round in combat and any other situation where the victim would be caught off guard.
Note that even in the worst cases of surprise attacks, the victim still gets a Saving Throw. The victim is denied a Saving Throw only if the Save is impossible to make, such as dodging a Dragon’s breath weapon while caught in its teeth, or avoiding a magical energy weapon while frozen in place from another spell.
There are no penalties for surprise for any other Saving Throw type. Poison doesn’t work faster on a surprised person, and the body and mind still resists System Shock, Spiritual Powers, Sleep/Charm, and Death Magic the same, regardless of surprise attacks.