PCIe freezes only when performing multiple back to back reads

I have modified Altera's high-performance SDRAM reference design to issue commands and read back acquired data using Stratix II GX DK. Everything works fine when iteratively issuing commands and capturing data. But, when I try to issue command once and perform back-to-back multiple reads, PCIe freezes after a random number of operations. I used Jungo's debug monitor and found that for reason instead of unlocking the previously held handle, driver just keep locking a new handle indefintely. Has anyone seen this problem or has any suggestion on what could be going wrong?

Thanks.