this image should illustrate what I am about to say...
[OBSERVE THE LEFT SIDES FOR THE MARKINGS ON THE PCI-E SLOTS]
Some slots below the slot nearer the CPU socket are often slower in bandwidth... so just check this or else you will see a drop... BY 50% in performance... and
I did see this myself before... I had an ABIT FATAL1TY FP-IN9 and the first slot was X16 in single but then if I stuck a card in the second they both became X8 and I do not remember what happened if I only used the second one but if your slot is specifically marked X8 then it will be X8... oh I recall now that my second slot was fixed X8 only... so just be sure of this before changing over... if you are stuck just tell us your mother board make and we can advise better
EDIT
Yes I do have am obsession with Capital I's
EDIT
Also observe the difference in Colour
EDIT
Also Notice the bottom one is X4 this is common and often the GPU places here is used for physx enhancement