I had the same problem (having to use a different version from the one officially available), so I installed the desired Boost version in a different directory (/opt/boost_1_51_0) and then used --with-boost=/opt/boost_1_51_0. It works flawlessly.
I'm not an autotools expert and I didn't do anything except for using the supplied macros. You can take a look at the projects files at https://github.com/avishorp/mksd

Avishay

2012/10/13 Mateusz Loskot <mateusz@loskot.net>
On 13 October 2012 13:20, Joost Kraaijeveld <J.Kraaijeveld@askesis.nl> wrote:
> On Sat, 2012-10-13 at 13:00 +0100, Mateusz Loskot wrote:
>> On 13 October 2012 12:57, Joost Kraaijeveld <J.Kraaijeveld@askesis.nl> wrote:
>> > Thanks for the reply but these three FAQs do not have the answer, I am
>> > afraid. The fist question is about an installed version of Boost.
>> > [...]
>>
>> It says:
>>
>> "If you have a staged boost library (still not installed) please
>> specify $BOOST_ROOT
>> in your environment and do not give a PATH to --with-boost option."
>
> No, that did not work either. This works if no installed Boost version
> is available, not if an installed version *is* available. This I
> experienced by trying.


I admit I haven't used autotools lately, so haven't tracked
status of the macro for Boost lookup.
But, I'm fairly sure the BOOST_ROOT and --with-boost-libdir
usually does the trick

        --with-boost=/custom/path/to/boost/root
        --with-boost-libdir=/custom/path/to/boost/root/lib

However, the macro tends to be iffy, and there are plenty of
bug reports for various distributions.

Best regards,
--
Mateusz Loskot, http://mateusz.loskot.net
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