I originally found the problem with clang, but have verified it with valgrind. A parameter is being freed by CCTK_SetString() in Misc.c, but is reused by CarpetIOHDF5. To reproduce, I build with clang, after commenting out the papi and hwloc thorns. Commenting out the call to free in CCTK_SetString() reveals alignment errors in LoopControl. I'm attaching the cfg file I used to build with clang.