I also had this happen when upgrading to SS4 on some of the my projects. My problem was caused by having some PCF files with an older version of the "SUE Inclusion" lines at the bottom. I was able to fix it by copying the new SUE Inclusion lines from the current examples project into my older PCFs or by commenting out the following lines in the older PCF files:
#----------------------------------------------------------------------------------------
# SUE Inclusion
#----------------------------------------------------------------------------------------
#%if defined (MSSUE_APPDIR)
# %include $(MSSUE_APPDIR)/SubsurfaceUtilitiesSamples.cfg
#%endif
#----------------------------------------------------------------------------------------
# SUE Inclusion
#----------------------------------------------------------------------------------------
#%if defined (MSSUE_APPDIR)
# %include $(MSSUE_APPDIR)/SubsurfaceUtilitiesSamples.cfg
#%endif