I'm certainly not an expert on RTLinux, but my thoughts are that somewhere in the Makefile it captures your architecture (x86_64) and then proceeds to try and find it in the source. I don't have a copy of the source, but I would presume that your architecture does not exist in a source that old.
You will probably be better off taking a look at
RTwiki or
Wind River:RTLinuxFree. This is much more up to date material and more likely to run on your hardware.