I have ported and created several low-level C-libraries to Android for my use in my application. I cross-compiled them using the NDK, and then link to them using System.loadLib
You can use the sequoyah project via eclipse to debug native code, it was a real pain for me to set this up and get it to work, I don't remember all the steps, but it's doable
Use ARM CE5 Community edition tools for eclipse and can debug any native code
I have asked something like this How to compile library with source code with NDK tools? My suggestion is deassembling with source code, then everything will be easy.
Try using NDK-STACK with the logcat output, it will at least tell you what file is the culprit and also the function.
https://developer.android.com/ndk/guides/ndk-stack
If your application is truly crashing in native code, I highly recommend the following:
At any rate, you should be able to fully debug native code and catch problems via ndk-gdb. You can find specific documentation on the ndk's version of gdb in your local installation of the ndk (for example, on my machine it's here):
android-ndk-r6/documentation.html
Finally, here's a basic tutorial on gdb:
gdb tutorial
Hope this helps!