rgd1101 :
what is the make and model of the motherboard?
if it really running at x2. it only about 8 times less than what it should be
The PCIe 2.0 x16 (x2 bandwidth) means the slot is physically x16 but electrically x2. Since this is PCIe 2.0 not PCIe 3.0 it is the same as a PCIe 3.0 x1 slot. This means it has 1/16th the bandwidth (except that PCIe 3.0 x1 isn't *exactly* PCIe 2.0 x2).
Technically 8 times less would mean it has negative bandwidth, right, if x16 is 15.75GB/s for PCIe 3.0 then 8 times less would be 126GB/s less or -110.25GB/s. Really this slot would have 1GB/s, so 1/15.75th which is very close to 1/16th (within 2%). A loss of 93.6% of the bandwidth.
OP: Your card should have 15.75GB/s of bandwidth. That other slot has 1GB/s of bandwidth. It's the same as a PCIe 1.0 x4 slot. This is enough to impact your gaming performance on the order of 5% in the worst case scenario. While it will work, the top slot is connected to your GPU and the bottom slot is connected to the chipset which is connected to the GPU. Using the bottom slot introduces this extra layer of communication and forces all of that PCIe data to be transferred via the link between the the CPU and the chipset which is shared with
every other device in your PC -- all your SATA drives, all your USB devices. It could be far worse than simply a PCIe 3.0 x1 slot connected directly to the CPU, which is already enough to cause a 5% drop.