What x4 card do you have, and what chipset is on it? The problem may be the card, not the slot. Just because the card has an x4 connector does not automatically mean that a single drive has access to all of that bandwidth.
Edit: Never mind, I didn't realize that this was a PCIe based drive on a card. I thought you were using an x4 PCIe SATA adapter.
Edit 2: What are you using to benchmark it?
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