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binutils 2.7 mipsorion64-elf question

I am trying to verify that the newly submitted mips port of rtems 
compiles and was merged correctly and may have tripped across a problem:

The submitter was using the very old "cygnus-2.6.4-950101" whatever that is.

I am using binutils 2.7 and gcc 2.7.2 snapshot 960719 configured for 
mips64orion-rtems which is a clone of mips64orion-elf.

The warning from ld is:

liblnk.rel: uses different e_flags (0x0) fields than previous modules 
clock.rel: uses different e_flags (0x1) fields than previous modules 

I can't explain the reason why sometimes it is a 0x0 and sometimes it is 
a 0x1 but I think that all of the files with this problem were generated
using "ld -r".

Does this sound like a known/familiar problem or do you need some more 
information from me?