I just tried to reproduce it again (make distclean/configure/make, with
enabled perl), and indeed, I got this on the second make run:

   Makefile:594: warning: overriding commands for target `makefile.mingw'
   Makefile:322: warning: ignoring old commands for target `makefile.mingw'
   rm -f libgimpi.a
   ar cru libgimpi.a gimpenv.o gimpchainbutton.o gimpcolorbutton.o gimpcolorspace.o 
gimpdialog.o gimpfileselection.o gimphelpui.o gimpmatrix.o gimppatheditor.o 
gimppixmap.o gimpprotocol.o gimpquerybox.o gimpsignal.o gimpsizeentry.o gimpunitmenu.o 
gimputils.o gimpvector.o gimpwidgets.o gimpwire.o gimpparasite.o gimpparasiteio.o 
   ranlib libgimpi.a
   make[2]: Leaving directory `/localvol2/cvs/gnome/gimp/libgimp'
   Making all in app
   Makefile:599: warning: overriding commands for target `makefile.mingw'
   Makefile:351: warning: ignoring old commands for target `makefile.mingw'
   /bin/sh ../libtool --mode=link gcc  -g -Os -g -pipe -mpentium -mcpu=pentium -Wall  
-o gimp -export-dynamic -export-symbols ./gimp.sym about_dialog.o airbrush.o 
app_procs.o asupsample.o batch.o bezier_select.o blend.o blob.o boundary.o 
brightness_contrast.o brush_edit.o brush_scale.o brush_select.o brush_select_cmds.o 
brushes_cmds.o bucket_fill.o by_color_select.o channel.o channel_cmds.o 
channels_dialog.o channel_ops.o channel_ops_cmds.o clone.o color_area.o 
color_balance.o color_cmds.o color_notebook.o color_panel.o color_picker.o 
color_select.o color_transfer.o colormaps.o colormap_dialog.o commands.o 
context_manager.o convert.o convert_cmds.o convolve.o crop.o cursorutil.o curves.o 
datafiles.o desaturate.o devices.o dialog_handler.o disp_callbacks.o display_cmds.o 
docindex.o dodgeburn.o draw_core.o drawable.o drawable_cmds.o edit_cmds.o 
edit_selection.o ellipse_select.o eraser.o errorconsole.o errors.o equalize.o 
fileops.o fileops_cmds.o flip_tool.o floating_sel.o floating_sel_cmds.o 
file_new_dialog.o free_select.o fuzzy_select.o gdisplay.o gdisplay_color.o 
gdisplay_color_ui.o gdisplay_ops.o general.o gimage.o gimage_mask.o gimpbrush.o 
gimpbrushgenerated.o gimpbrushlist.o gimpbrushpipe.o gimpcontext.o 
gimpcontextpreview.o gimpdnd.o gimphelp.o gimphistogram.o gimplist.o gimplut.o 
gimpparasite.o gimpprogress.o gimprc.o gimprc_cmds.o gimpui.o gimpunit.o global_edit.o 
gradient.o gradient_select.o gradient_select_cmds.o gradients_cmds.o gtkwrapbox.o 
gtkhwrapbox.o gtkvwrapbox.o guides_cmds.o gximage.o help_cmds.o histogramwidget.o 
histogram_tool.o hue_saturation.o image_cmds.o image_map.o image_new.o image_render.o 
indicator_area.o info_dialog.o info_window.o ink.o interface.o internal_procs.o 
invert.o iscissors.o layer.o layer_cmds.o layer_select.o layers_dialog.o lc_dialog.o 
levels.o lut_funcs.o magnify.o main.o measure.o menus.o message_cmds.o misc_cmds.o 
module_db.o move.o nav_window.o ops_buttons.o palette.o palette_cmds.o 
palette_select.o paint_core.o paint_funcs.o paintbrush.o parasite_cmds.o 
parasitelist.o path.o paths_cmds.o paths_dialog.o pattern_select.o 
pattern_select_cmds.o patterns.o patterns_cmds.o pencil.o perspective_tool.o 
pixel_processor.o pixel_region.o plug_in.o plug_in_cmds.o posterize.o 
preferences_dialog.o procedural_db.o procedural_db_cmds.o qmask.o rect_select.o 
regex.o resize.o rotate_tool.o scale.o scale_tool.o scan_convert.o scroll.o 
selection.o selection_cmds.o session.o shear_tool.o smudge.o temp_buf.o text_tool.o 
text_tool_cmds.o threshold.o tile.o tile_cache.o tile_manager.o tile_swap.o 
tips_dialog.o tool_options.o tools.o tools_cmds.o transform_core.o transform_tool.o 
undo.o undo_cmds.o undo_history.o unit_cmds.o user_install.o xcf.o libgimpim.a         
../libgimp/libgimpi.a           -L/usr/app/lib -L/usr/X11R6/lib -lgtk -lgdk -rdynamic 
-lgmodule -lglib -ldl -lXi -lXext -lX11 -lm                                            
                           -lpthread                                        
-L/usr/app/lib
   gcc -g -Os -g -pipe -mpentium -mcpu=pentium -Wall -o gimp about_dialog.o airbrush.o 
app_procs.o asupsample.o batch.o bezier_select.o blend.o blob.o boundary.o 
brightness_contrast.o brush_edit.o brush_scale.o brush_select.o brush_select_cmds.o 
brushes_cmds.o bucket_fill.o by_color_select.o channel.o channel_cmds.o 
channels_dialog.o channel_ops.o channel_ops_cmds.o clone.o color_area.o 
color_balance.o color_cmds.o color_notebook.o color_panel.o color_picker.o 
color_select.o color_transfer.o colormaps.o colormap_dialog.o commands.o 
context_manager.o convert.o convert_cmds.o convolve.o crop.o cursorutil.o curves.o 
datafiles.o desaturate.o devices.o dialog_handler.o disp_callbacks.o display_cmds.o 
docindex.o dodgeburn.o draw_core.o drawable.o drawable_cmds.o edit_cmds.o 
edit_selection.o ellipse_select.o eraser.o errorconsole.o errors.o equalize.o 
fileops.o fileops_cmds.o flip_tool.o floating_sel.o floating_sel_cmds.o 
file_new_dialog.o free_select.o fuzzy_select.o gdisplay.o gdisplay_color.o 
gdisplay_color_ui.o gdisplay_ops.o general.o gimage.o gimage_mask.o gimpbrush.o 
gimpbrushgenerated.o gimpbrushlist.o gimpbrushpipe.o gimpcontext.o 
gimpcontextpreview.o gimpdnd.o gimphelp.o gimphistogram.o gimplist.o gimplut.o 
gimpparasite.o gimpprogress.o gimprc.o gimprc_cmds.o gimpui.o gimpunit.o global_edit.o 
gradient.o gradient_select.o gradient_select_cmds.o gradients_cmds.o gtkwrapbox.o 
gtkhwrapbox.o gtkvwrapbox.o guides_cmds.o gximage.o help_cmds.o histogramwidget.o 
histogram_tool.o hue_saturation.o image_cmds.o image_map.o image_new.o image_render.o 
indicator_area.o info_dialog.o info_window.o ink.o interface.o internal_procs.o 
invert.o iscissors.o layer.o layer_cmds.o layer_select.o layers_dialog.o lc_dialog.o 
levels.o lut_funcs.o magnify.o main.o measure.o menus.o message_cmds.o misc_cmds.o 
module_db.o move.o nav_window.o ops_buttons.o palette.o palette_cmds.o 
palette_select.o paint_core.o paint_funcs.o paintbrush.o parasite_cmds.o 
parasitelist.o path.o paths_cmds.o paths_dialog.o pattern_select.o 
pattern_select_cmds.o patterns.o patterns_cmds.o pencil.o perspective_tool.o 
pixel_processor.o pixel_region.o plug_in.o plug_in_cmds.o posterize.o 
preferences_dialog.o procedural_db.o procedural_db_cmds.o qmask.o rect_select.o 
regex.o resize.o rotate_tool.o scale.o scale_tool.o scan_convert.o scroll.o 
selection.o selection_cmds.o session.o shear_tool.o smudge.o temp_buf.o text_tool.o 
text_tool_cmds.o threshold.o tile.o tile_cache.o tile_manager.o tile_swap.o 
tips_dialog.o tool_options.o tools.o tools_cmds.o transform_core.o transform_tool.o 
undo.o undo_cmds.o undo_history.o unit_cmds.o user_install.o xcf.o libgimpim.a 
../libgimp/libgimpi.a -L/usr/app/lib -L/usr/X11R6/lib -lgtk -lgdk -rdynamic -lgmodule 
-lglib -ldl -lXi -lXext -lX11 -lm -lpthread -L/usr/app/lib -Wl,--export-dynamic

The overriding warnings are probably not relevent (I get them in a couple
of directories).

This is indeed unrelated to the parallel build problem. And indeed also
happens on my machine ;)

-- 
      -----==-                                             |
      ----==-- _                                           |
      ---==---(_)__  __ ____  __       Marc Lehmann      +--
      --==---/ / _ \/ // /\ \/ /       [EMAIL PROTECTED] |e|
      -=====/_/_//_/\_,_/ /_/\_\       XX11-RIPE         --+
    The choice of a GNU generation                       |
                                                         |

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