When linking my project in the release mode I am getting the following warning:
myProject-libs/release/libboost_regex-mt-s-1.50.0.a(cpp_regex_traits.o): dupl
Your compilers were compiled with different options :) Compiling the library on Linux and the program on Windows result in a situation where there is an identically named .data segment, but they aren't the same size. That could theoretically be interesting, inasmuch as a data segment is writable, but in practice, it shouldn't matter. Unless there is evidence to suggest this causes a problem of which I'm not aware, you can safely suppress that warning; I don't know how you'd make it go away, though.
I recently encountered this problem (i.e. linker warning "duplicate section has different size") when trying to compile boost for Windows using mingw.
The issue I had was that I compiled my application with -std=c++14 but when compiling boost I didn't specifically provide a dialect flag (which defaulted to -std=c++98 for g++ 5.3.0). Adding the dialect flag -std=c++14 when compiling boost solved the problem for me. See this answer for an explaination on how to set cxxflags when compiling boost.
I believe my solution might have worked for you (your application was compiled with -std=c++0x but boost was not provided any dialect flag). Although I am 6 years too late, I'll leave my answer here for others who happen to stumble-upon this issue.