Simply, a .so compiled by android ndk r9 gcc 4.6 crashed on loading in function __check_for_sync8_kernelhelper.
After looking up the issue in Google, I found this issue has been reported to Google: https://code.google.com/p/android/issues/detail?id=58476. Unfortunately no solution at present.
Basically it is an libgcc issue depending on linux kernel version. Lower kernel version lacks the symbol that libgcc in 4.6 or higher needs. For example, the Galaxy Nexus I am just testing app on.
1) Avoid using 64bit atomic operation built in gcc, if you can control everything in your codes.
2) Using gcc 4.4.3. For ndk r9 there is a legacy toolchain package in a separated download link.