Maybe you guys can solve this for me: PCI-e x16 slot issue

I have an ASRock Z68 Xtreme 3 Gen 3 board, which I'm hoping to upgrade soon to a Z77-based board. (Hence, my previous thread in this same forum from a few weeks ago.)

I have two PCI-e x1 cards-- an Intel Gigabit CT and a SATA expansion card.

Here's the issue:

• Plugging in the Gigabit CT card in the only available x1 slot (the other one is blocked by the video card), Intel's official drivers recognize it. perfectly.
  
  Plugging it into the second available x16 slot, Intel's drivers do not recognize it as a valid Intel NIC but Windows 8.1 drivers does see it as a bog-standard Intel gigabit NIC.
  
  However, while in the other x16 slot, the connection drops continuously which doesn't show this issue in the x1 slot.
• The Marvell-based SATA expansion card plugged in the x1 slot is recognized perfectly, but in the second x16 slot it is recognized but the card has a habit of "disappearing" in the Device Manager.

The issue further complicates itself when I compare it between my experience in Windows 7 and 8.1 Pro:

• Under Windows 7, the Gigabit CT card is recognized perfectly by both the Intel and Windows drivers as an an Intel NIC regardless if it's plugged in the x16 or x1 slot.
• Under Windows 7, an older SATA (Silicon Imaging-based) expansion card would prevent Windows from booting up at all if it's in the x16 slot, but will boot normally if in the x1 slot. The newer Marvell-based card allows Windows to boot in either the x16 or x1 slot, but still exhibits a disappearing act if it remains in the x16 slot.

So, is this a bad secondary x16 slot on this board?

Or, is Windows 7/8.1 doing something funny at trying to recognize what is what in either slot?

This is one other reason I was asking earlier what's a good Z77 board with enough PCI-e x1 slots or the x16 slots support x1 cards without issue. (And, stable enough to last 3 to 5 years.)

Thank you for replying.

(Note: I've already tried updating to the latest available Intel chipset drivers by Intel but it has not fixed the issue.)

Funnily enough, with an older MSI 790X-based AMD board, I did not have these issues under Windows 7 with either the Gigabit CT or SI-based SATA expansion card. The x16 slot allowed both booting to Windows and having both cards recognized and working perfectly by the drivers.