I've noticed that some Intel and Server Works based motherboards have PCI-X slots that are in the same bus. Will the speed of one slot affect the others?
Yes, it will. For example, X5DA8 has 3 64-bit PCI-X slots, 2 of them are in the same bus of the P64H2 chip and that results in each slot can only runs at 100MHz max. If you are using a 66MHz card in one of these slots, then both slots will be at 66MHz max.