Steve:
I had the same problem back in 5.0. I had hoped that this would have been fixed in 5.1...oh well.
Add the -G0 option to the ECOS_GLOBAL_CLAGS = .... either in your makefile or in the Global Build Options within the configuration tool.
Here is an explaination of the flag from the ld doc located at:
C:\altera\kits\nios2_51\documents\gnu-tools\binutils -Gvalue
--gpsize=value
Set the maximum size of objects to be optimized using the GP register to size. This is only meaningful for object file formats such as MIPS ECOFF which supports putting large and small objects into different sections. This is ignored for other object file formats.
Hope this work......by the way...any luck getting compact flash to work?
Graham......