libtool version mismatch error persists after running `autoreconf -fvi`

Question

I'm trying to add a new binary to an old project written in C/C++ on my machine with Ubuntu 14.04. First I need to run ./setup_configure which runs the following script:

  #!/bin/tcsh -f                                                                                                                                                               
  2 
  3 # For a new dev/ environment, before running configure, 
  4 # and anytime after a Makefile.am file has changed, 
  5 # the following commands must be executed within the 
  6 # dev/ directory:
  7 
  8 set cmd1=(rm -rf autom4te.cache)
  9 if ( "`uname -s`" == "Darwin" ) then 
 10     set cmd2=(glibtoolize --force)
 11 else
 12     #set cmd2=(libtoolize --force)
 13     set cmd2=(libtoolize -f -v)
 14 endif
 15 set cmd3=(aclocal)
 16 #automake --add-missing is necessary because config.sub
 17 # and config.guess are links, and make not be present,
 18 # so if missing, --add-missing will add them for this
 19 # platform
 20 #set cmd4=(automake --add-missing -Wno-portability)
 21 set cmd4=(automake -a -c)
 22 set cmd5=(autoreconf --force -Wno-portability)
 23 #automake Note: autoreconf --force runs automake
 24 set cmd6=(autoconf -Wno-portability)
 25 
 26 echo $cmd1
 27 $cmd1
 28 if ($status) exit $status
 29 echo $cmd2
 30 $cmd2
 31 if ($status) exit $status
 32 echo $cmd3
 33 $cmd3
 34 if ($status) exit $status
 35 echo $cmd4
 36 $cmd4
 37 #if ($status) exit $status
 38 echo $cmd5
 39 $cmd5
 40 if ($status) exit $status
 41 echo $cmd6
 42 $cmd6
 43 if ($status) exit $status
 44 
 45 # The first three commands create the platform specific 
 46 # tools needed by configure (use glibtoolize on the Mac 
 47 # in place of libtoolize). These platform specific tools 
 48 # are placed in the dev/config directory. 
 49 # Autoreconf --force and automake create the Makefile.in 
 50 # files from the Makefile.am files in each directory. 
 51 # Following successful execution of these commands, the 
 52 # configure command can be executed. 
 53 

and afterwards I need to run ./configure. Since I do not want to compile the whole project I cd into the new sub-directory I have added and run make, however, the process does not go smoothly and ends with the following error:

/bin/bash ../libtool  --tag=CC   --mode=link g++ -I../include   -L/usr/lib64 -L/usr/X11R6/lib64     -L/opt/mni_library/lib -L/opt/vxl/build/lib    -o mri_segment_ms mri_segment_ms.o ../utils/libutils.a ../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lz -lm -lcrypt -ldl -lpthread     -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib 
../libtool: line 469: CDPATH: command not found
libtool: Version mismatch error.  This is libtool 2.4.2 Debian-2.4.2-1.7ubuntu1, but the
libtool: definition of this LT_INIT comes from an older release.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 Debian-2.4.2-1.7ubuntu1
libtool: and run autoconf again.
make: *** [mri_segment_ms] Error 63

I have found lots of Q&As regarding a similar problem over internet, most of which suggest the user to run autoreconf -ivf. There is also a comprehensive answer in Stackoverflow here and here. I have performed all the suggested steps, unfortunately the problem persists. I was wondering whether anyone could give me a hint.

EDIT: the same thing happens if I try to make from root directory of the whole project.