Wheels can vary far more than most drivers realise as different makes, different offsets and different materials all have a substantial effect on performance.
Many rims look similar but may be of different manufacture. Be sure to check that your rims are matched and that any replacements or alternatives are correct. You may find advantages in using different rims but it's a common mistake to test on one type then race another requiring comletely different setup.
Magnesium rims are not chosen for weight saving but more for consistency; they dissipate heat better than aluminium and therefore the air pressure inside them does not increase so much. You may find that you can use a slightly higher cold pressure without the degradation in performance inherant with aluminium rims once the tyres exceed their optimium temperature.
The offset of rims will also affect performance; those with a deeper offset will need the hubs to be moved outwards to achieve the same overall track measurement. This means that you are exposing more of the axle which has a similar effect to using a different grade of axle or different hubs.