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I need to install Python 2.7 in two architectures, but under one file system. I thus configure:
/home/cellnet/michaelk/SRC/Python-2.7.3> ./configure --prefix=/home/cellnet/michaelk/biocluster --exec-prefix=/home/cellnet/michaelk/biocluster -q
When I compile and then run "make install", it will try to copy libraries to "/home/cellnet/michaelk/lib64/python", i.e. it will try to copy files outside the specified prefixes. The step is "make sharedinstall", which fails because I've temporarily made the lib64 directory read-only: 
[michaelk@biocluster2] /home/cellnet/michaelk/SRC/Python-2.7.3> make sharedinstall
running build
running build_ext
building dbm using bdb
Python build finished, but the necessary bits to build these modules were not found:
bsddb185 dl gdbm 
imageop sunaudiodev 
To find the necessary bits, look in setup.py in detect_modules() for the module's name.
running build_scripts
./python -E ./setup.py install \
 --prefix=/home/cellnet/michaelk/biocluster \
 --install-scripts=/home/cellnet/michaelk/biocluster/bin \
 --install-platlib=/home/cellnet/michaelk/biocluster/lib/python2.7/lib-dynload \
 --root=/
running install
running build
running build_ext
building dbm using bdb
Python build finished, but the necessary bits to build these modules were not found:
bsddb185 dl gdbm 
imageop sunaudiodev 
To find the necessary bits, look in setup.py in detect_modules() for the module's name.
running build_scripts
running install_lib
copying build/lib.linux-x86_64-2.7/_ctypes.so -> /home/cellnet/michaelk/lib64/python
error: could not delete '/home/cellnet/michaelk/lib64/python/_ctypes.so': Permission denied
make: *** [sharedinstall] Error 1

Sorry, I'm unable to reproduce your results and they look rather suspicious. Keep in mind that the Python build uses its copy of Distutils to build and install the interpreter's shared extension modules, like _ctypes.so. My guess is that your "make install" is being influenced by settings in a Distutils configuration file, such as ~/.pydistutils.cfg. If so, this is a duplicate of Issue4655.
http://docs.python.org/2/install/index.html#distutils-configuration-files 

Thanks a lot Ned: you're right, the unexpected path was indeed set in ~/.pydistutils.cfg. So I agree with what has been written in the other issues, that the installation should detect the clash between the command line configuration and the configuration file to alert the unsuspecting user.