I've got gcc-4.4, gcc-4.5 and gcc-4.6 installed from Debian's repositories. That's the only source of multiple runtimes that I can think of. I can uninstall older compilers, but it may be better to figure out what exactly is going on and prevent it from happening.
I do not switch between them in any way. I've configured gnustep-make without explicitly specifying a compiler. gcc --version says that I'm running gcc-4.6.
Do you have any ideas how I can check which runtime is being used at which stage?
Once again, I can be on XMPP later today if someone is interested in helping me debug this. I can probably rig up some sort of SSH access to the machine, as well.