I regularly rebuild synfig from source. Each time I 'make install', it re-links and re-installs all the modules, whether or not they have changed. To stop this happening, I modified one of the automake files.
Here's a patch for automake-1.9.
Here's a patch for automake-1.10.
Now modules are only re-linked and re-installed when they need to be.
It's kind of ugly to hack automake like this, but it works for me. There's probably a nice way to achieve the same effect.