I thought with more info I might've been able to help but after looking at your output, I think I'm out of my depth on this one. Sorry about that.
I also didn't pick up earlier on the fact that you're using C++ for your application... right now C++ isn't officially supported by us with Nios II Linux because of compiler issues. The compiler that ships with the Nios II v5.0 is compiled against newlib and we use uClibc by default.
While I don't understand all the details, I've been told by my co-workers that the iostream functionality in C++ is broken for Nios II Linux due to how gcc was compiled (i.e., against newlib vs. uClibc). I've also been told that the STL also doesn't work.
I hope the warning doesn't come to late. Perhaps others out there have been able to successfully get C++ working with Nios II Linux?