Could you be a little more specific about the issues you've heard?
I ran the PCIe tests from one of the Altera app notes (PCIe to memory design I believe), and I'm pretty sure some of the examples worked; where 'working' meant that I saw the devices on the PCI bus under Windows. I didn't perform more complete tests, as I didn't have time. I was more interested in checking that my laptop ExpressCard-to-PCIe x1 adapter interfaced to the PCIe motherboard in which I had the S4GXDK installed.
The laptop was loaded with Windows 7 64-bit. I didn't try accessing the S4GXDK board, since I think the Jungo drivers that Altera supplies only works under Windows 32-bits. At some point, I'll put Linux on the laptop, and then use sysfs file system nodes to perform read/write accesses on the bus, or write a Linux driver.
The Altera Wiki has a PCIe example that looks nice. I'd take a look at that.
Cheers,
Dave