iproute won't emerge with vanilla kernel

[KrakHed]

I'm trying to install fwbuilder through portage but one of the dependencies is iproute which won't compile. Searching around I have found some people mentioning that its probably related to the kernel source I have installed. I'm not using the gentoo kernel right now as I have compiled up my own with some other oddities in it. Is this probably related? What should I do about it? I'm able to compile up fwbuilder if I grab the source and do it manually but I really like the version tracking that portage offers and would rather use that. Any suggestions?
Also, if I compile up something manually, where do I put the lib lines that I would normally append to /etc/ld.so.conf? I can't but them there in gentoo because it is overwritten during emerges.
Thanks for a quality distro. I was a huge fan of mandrake right up until the day I used gentoo for the first time.