Eagle needs to be run as "root" first, in order to have write access 
to %%PREFIX%%/share/eagle to write a program key file.

Once this has been done, you can delete the "eagle" directory in your 
/root directory, which is created during the initially startup, and 
run it as a normal user.

It is entirely possible that you need linux 2.6 emulation support
in the kernel.  The /usr/ports/UPDATING entry on 20080318 has
good instructions on how to run linux 2.6.16 kernel emulation.