emerge failure with mpir due to absolute path in configure line

[ostroffjh]

(apologies for bad formatting from webmail)

 I know I've run into this problem before, but I absolutely can't  remember how I solved it in the past, and I can't find anything with Google.  The issue is that during the configure, it gets:
 checking size of mp_limb_t... 0
 configure: error: Oops, mp_limb_t doesn't seem to work
What I do find is that this seems to be due to the configure line using absolute paths instead of just ./configure, even though it does cd to the working directory first.
 
This is with a relatively new install from scratch, including msys, as I have a vague memory of needing to update msys for this or some other problem.  I also know I could manually launch msys and do the ./configure, but I've always had trouble getting emerge to finish the rest of the steps without starting from scratch and overwriting what I've already done.
 
Thanks for any suggestions, or pointers to a solution I missed.
 
Jack