OK, so adjoints_ex1 on the automake branch works just fine in DEBUG mode. This is consistent with trunk, and what we've seen with hand-built compilers and non-libtool linking all along... so no better stack traces unfortunately.
Pressed "send" too soon... miscellaneous_ex6 fails in debug mode on the automake branch. (This is also consistent with what we see on trunk.) The stack trace is below. You can see that things go awry as soon as it tries to call down into a C library routine in triangle. Again, I "fixed" this on trunk by modifying triangle's Makefile to use libtool.
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: 13 at address: 0x0000000000000000
0x00007fff948218a5 in misaligned_stack_error_entering_dyld_stub_binder ()
#0 0x00007fff948218a5 in misaligned_stack_error_entering_dyld_stub_binder ()
#1 0x00007fff5fbea5d0 in ?? ()
#2 0x000000010169ac38 in bswpiv.1559 ()
#3 0x000000010090f545 in triangulate (triswitches=0x102f08448 "zBPQqpa0.010000", in=0x7fff5fbfeaa0, out=0x7fff5fbfeb50, vorout=0x0) at triangle.c:15726
#4 0x00000001005308e1 in libMesh::TriangleInterface::triangulate (this=0x7fff5fbfee90) at src/mesh/mesh_triangle_interface.C:323
#5 0x0000000100001fb3 in triangulate_domain () at miscellaneous_ex6.C:153
#6 0x0000000100001998 in main (argc=1, argv=0x7fff5fbff1c0) at miscellaneous_ex6.C:62