PCI Express Tx interface gets stalled

No, I wouldn't expect that to be the case. Assuming a 4KB page, the 12 LSBs of a page address are guaranteed to be '0', which also guarantees that the same address is QWORD aligned.

I have successfully done exactly what you are trying to do with both the PCIe high performance reference design and a home brew design, both running on the Stratix IV dev kit. I have also successfully run the Altera design under Windows using the reference design drivers and code and under Linux using a custom driver and application. I have only run the home brew design under Linux.