I'm not an FSO dev and am not that familiar with the codebase, but I'll take a look. Hopefully an Linux FSO coder can chime in with their opinion at some point.
Are you building from trunk, or from a source tarball? If from trunk, could you type
svn up
at the prompt while you're at your fs2_open root-level source directory, to make sure your local copy of the source is up-to-date? After doing that, could you try compiling again?
EDIT: You may have better luck with building from a source tarball, since those have been tested to ensure that they compile. AFAIK, SCP doesn't guarantee that trunk will always be compilable on every platform. The latest release candidate thread (RC6) is
here. Look for "Source Code Export".