Of course your frame rates are lower, you went from a BX mobo to a VIA 133A mobo! The BX chipset has the edge in both memory and AGP bandwidth, so you should have expected a drop in fps.
1.Old Antec Case, Asus PC-DL, 2 x 1.6 LV D1 Xeons @ 3 GHz, 2GB Corsair PC3200 @ 200 MHz, Chaintech 6800 128MB AGP
2. Old Crap Beige Case, Gigabyte GA-H55M-S2H, Core i3 530, 4GB CL8 OCZ DDR3-1600, eVGA GTX465
3. Asus Pundit mATX Case, MSI AMD Zacate E350/dual core E350IS-E45 mini-ITX, 4GB CL9 Crucial Ballistix DDR3-1333, LG Blu Ray/HD DVD & DVD Burner