Configure script:

#! /bin/ksh -px

export PATH=/cadappl/bin:/opt/aCC/bin:$PATH
export LPATH=/usr/lib:/cadappl/mysql/3.22.32/lib:/nlww/user1/apache/pdflib/lib:/
cadappl/tifflib/3.5.4/lib:/cadappl/jpeglib/6b/lib:/cadappl/pnglib/1.0.8/lib:/cad
appl/zlib/1.1.3/lib:/

./configure \
  --prefix=/nlww/user1/apache/php \
  --with-apxs=/nlww/user1/apache/bin/apxs \
  --with-config-file-path=/nlww/user1/apache/php/lib \
  --enable-safe-mode \
  --with-mysql=/nlww/user1/apache/mysql\
  --with-pdflib=/nlww/user1/apache/pdflib \
  --with-zlib-dir=/cadappl/zlib/1.1.3 \
  --with-jpeg-dir=/cadappl/jpeglib/6b \
  --with-png-dir=/cadappl/pnglib/1.0.8 \
  --with-tiff-dir=/cadappl/tifflib/3.5.4 \
  --with-zlib=/cadappl/zlib/1.1.3 \

When using version 4.0.4pl1 everything works fine.
Using version 4.0.6 apache won't start complaining it can't find the libraries of tifflib, zlib, etc.

Possible cause:
When using 4.0.6 libtool is generated different:
Output from diff 4.0.4pl1/libtool 4.0.6/libtool:

39c39
< # CC="cc" CFLAGS="-g" CPPFLAGS=" -DHPUX11 -D_HPUX_SOURCE -DUSE_HSREGEX -DUSE_EXPAT -DXML_BYTE_ORDER=21" \
---
> # CC="cc" CFLAGS="-g" CPPFLAGS=" -DHPUX11 -D_HPUX_SOURCE -DUSE_HSREGEX -DUSE_EXPAT -DSUPPORT_UTF8 -DXML_BYTE_ORDER=21" \
184c184
< deplibs_check_method="file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library"
---
> deplibs_check_method="unknown"
187c187
< file_magic_cmd="/usr/bin/file"
---
> file_magic_cmd=""

When editing libtool and changing deplibs_check_method and 
file_magic_cmd everything is going fine and the apache daemon will start.