When in doubt then perhaps it is a good idea to get rid of everything and start all over again.
That's what I decided to do when all of a sudden Komodo stopped working becuase of some linux emulation hiccup when I upgraded FreeBSD.
Have a look in the file
/usr/ports/UPDATING and this is what you see:
20060616:So that's what I did and things have improved greatly since then.
AFFECTS users of emulation/linux_base-*
We now use Fedora Core 4 as the linux base port, and the corresponding xorg libs for the linux X11 libs port.
To upgrade you have to run
portupgrade -f -o emulators/linux_base-fc4 linux_base\*
portupgrade -f -o x11/linux-xorg-libs linux-XFree86-libs
After this start a linux program to test, e.g., acroread. If you get errors when starting linux programs about problems with libraries, and you made sure no LD_* variable is set as described above, you are one of those unlucky people where we do not have a better solution as to tell you to deinstall every linux port, remove /compat/linux completely to make sure no cruft is left and reinstall everything you need.