pci bridge fpga card

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I have an AMIRIX board ap1070 .
There is a pci bridge (POWERSPAN II ) from TUNDRA on the board which
provides the interface communication between the fpga and the pci
card. The AMIRIX has given me the source code of the drivers in linux
but on windows they have just givenme a exe file which opens a gui
application to read and write into the fpga. I have made some changes
to the design to provide the ability to write bulk data into the fpga
bram. The design works fine with windows but then I donw havee source
code and hence cannot do any modifications on the host side. Where as
in Linux  whenever I run the driver program the system hangs. I dont
know why such a thing happens. Is there any good reference material or
standard for initializing the pci bridges?  Right now I am going
through the application note of powerspan II since I suspect that in
windowsthe pci bridge registers get programmed properly in windows and
in linux they dont.

In windows however

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