On Wed, Nov 7, 2012 at 4:40 PM, John Peterson <jwpeterson@gmail.com> wrote:

.) Do you know what magic libtool could possibly be doing here?

Sorry I haven't had time to look into it myself, but one of the things libtool will do is add flags in a system dependent way (and occasionally strip some out if you aren't careful and made a typo in an option or something). Again, I haven't had time to look, but if you feed configure --disable-silent-rules, this will produce verbose output during compile and linking. It will first show the lines that were passed to libtool and then show the line that it actually used. Doing a diff on those should help elucidate what's going on.
.) On the automake branch, I still get the (system-level) segfaults with my hand-built compilers.

What are the errors?
 Do you know how automake builds shared libraries?

libtool is what takes care of this. Again, you'll see the command it uses at link time with the --disable-silent-rules configure option.
 Is there any way I could try this libtool trick with the automake branch of libmesh as well?

libtool should be doing the "trick" you showed. So are you in the situation that trunk and branch are failing in different ways with hand-built GCC?