Finally after several days on looking into this issue I found the solution. It is as simple as stupid.
My original linker commandline looked like this:
g++ -shared -o mylib.so -L/usr/local/lib -lxerces-c objects...
Googling on this problem didn't yield anything usefull, so finally I decided to create a fresh new sample project with eclipse and suddenly it worked. The only difference was in the commandline to the linker. When I applied the same order to my main project it suddenly compiled.
g++ -L/usr/local/lib -shared -o mylib.so objects... -lxerces-c
Note that in the above line, the objects come before the library, and apperently this makes the difference. I thought that the ordering of the libs only applies to the libraries, but apparently also the objects must be ordered appropriately.