This layout is insisting my instance of DF is closed. It seems to be detecting it alright, but it thinks the dwarves are all outsiders, and therefore invalid. Here are the pertinent lines in the log:
2010-Jun-09 21:00:03.031 DEBUG found copy with HWND: 0x17041e [src\dfinstancewindows.cpp:202]
2010-Jun-09 21:00:03.031 DEBUG PID of process is: 1460 [src\dfinstancewindows.cpp:209]
2010-Jun-09 21:00:03.031 DEBUG PROC HANDLE: 0x4f8 [src\dfinstancewindows.cpp:217]
2010-Jun-09 21:00:03.031 DEBUG PEB is at: 0x7efde000 [src\dfinstancewindows.cpp:223]
2010-Jun-09 21:00:03.031 DEBUG read 12 bytes BASE ADDR is at: 0x400000 [src\dfinstancewindows.cpp:236]
2010-Jun-09 21:00:03.031 DEBUG Target EXE was compiled at "2010-06-09T08:06:45" [src\dfinstancewindows.cpp:70]
2010-Jun-09 21:00:03.031 DEBUG DF's checksum is: "0x4c0f83d5" [src\dfinstance.cpp:495]
2010-Jun-09 21:00:03.031 INFO Detected Dwarf Fortress version "v0.31.06 (graphics)" using MemoryLayout from "C:/Games/df/DwarfTherapist-0.5.3/etc/memory_layouts/windows/v0.31.06_graphics.ini"
2010-Jun-09 21:00:03.031 DEBUG base address: "0x00400000" [src\dfinstancewindows.cpp:254]
2010-Jun-09 21:00:03.031 DEBUG memory correction: "0x00000000" [src\dfinstancewindows.cpp:255]
2010-Jun-09 21:00:03.046 DEBUG Connection to DF version "v0.31.06 (graphics)" established. [src\mainwindow.cpp:252]
2010-Jun-09 21:00:03.046 DEBUG Loading language translation tables [src\dwarftherapist.cpp:304]
2010-Jun-09 21:00:03.046 DEBUG Loading generic strings from 16c53ac [src\dwarftherapist.cpp:317]
2010-Jun-09 21:00:03.046 DEBUG generic words 2107 [src\dwarftherapist.cpp:319]
2010-Jun-09 21:00:03.062 DEBUG FOUND LANG ENTRY 400fb50 "DWARF" [src\dwarftherapist.cpp:330]
2010-Jun-09 21:00:03.062 DEBUG FOUND LANG ENTRY 4accae8 "ELF" [src\dwarftherapist.cpp:330]
2010-Jun-09 21:00:03.062 DEBUG FOUND LANG ENTRY 4afac00 "GOBLIN" [src\dwarftherapist.cpp:330]
2010-Jun-09 21:00:03.062 DEBUG FOUND LANG ENTRY 4b28b38 "HUMAN" [src\dwarftherapist.cpp:330]
2010-Jun-09 21:00:03.062 DEBUG Loading dwarf strings from 400fba4 [src\dwarftherapist.cpp:335]
2010-Jun-09 21:00:03.062 DEBUG dwarf words 2107 [src\dwarftherapist.cpp:337]
2010-Jun-09 21:00:03.078 DEBUG Ignoring "Mebzuth Olonostuk" who appears to be "from the Underworld. SPOOKY!" [src\dwarf.cpp:323]
2010-Jun-09 21:00:03.078 DEBUG Ignoring "Tun Kerlîgakrul" who appears to be "from the Underworld. SPOOKY!" [src\dwarf.cpp:323]
2010-Jun-09 21:00:03.078 DEBUG Ignoring "Ingish Idenzasit" who appears to be "from the Underworld. SPOOKY!" [src\dwarf.cpp:323]
2010-Jun-09 21:00:03.078 DEBUG Ignoring "Nil Ilraliseth" who appears to be "from the Underworld. SPOOKY!" [src\dwarf.cpp:323]
2010-Jun-09 21:00:03.078 DEBUG Ignoring "Ast Mosusgeshud" who appears to be "from the Underworld. SPOOKY!" [src\dwarf.cpp:323]
2010-Jun-09 21:00:03.078 DEBUG Ignoring "Doren Vabôkìnal" who appears to be "from the Underworld. SPOOKY!" [src\dwarf.cpp:323]
2010-Jun-09 21:00:03.078 DEBUG Ignoring "Moldath Uzolróth" who appears to be "from the Underworld. SPOOKY!" [src\dwarf.cpp:323]
2010-Jun-09 21:00:03.078 INFO found 0 dwarves out of 45 creatures
2010-Jun-09 21:00:03.078 WARNING lost connection to DF [src\mainwindow.cpp:278] (lost_df_connection)
2010-Jun-09 21:00:03.093 DEBUG DFInstance baseclass virtual dtor! [src\dfinstance.cpp:103]
2010-Jun-09 21:00:03.609 INFO RUNNING VERSION : "0.5.3"
2010-Jun-09 21:00:03.609 INFO LATEST AVAILABLE VERSION: "0.5.3"
This is on Windows XP x64, 35.06 SDL, only change from pure vanilla (including tilesets, but not including game options) is a raws change to make hooves into shells.