It turns out that the root of the problem was in using Armadillo's .inv() function to invert complex matrices. Armadillo library outsources some of its linear algebra calculations to lapack, which should be no problem since R also relies on lapack (who doesn't, right?). But for some reason r-project.org systems have only an abbreviated version of the lapack library, missing some functions for complex matrix calculations. This problem is discussed here.
Following suggestions from the above link, my solution was to download missing fortran routines (zgetri.f, ztrti2.f, ztrtri.f) from http://www.netlib.org/lapack/ and add them to /src directory of our package. A bit ugly, but worked and the package compiled on R-forge on all architectures.
P.S. As of July 22, 2012, our
Update on the P.S.: It looks like the problem with the survival package was resolved by the R-forge compilers. Our cthmm compiles now.