I assume you have checked the output of phpinfo() and confirmed hat your setting of the $PHP_AUTOCONF variable actually *is being set as you expected/directed?
My only thoughts at this point are that possibly that variable is somehow set incorrectly for your installation (autoconf is not where it is expected) or a permission problem that is keeping autoconf from being read.
In addition to the PHP error output, have you checked you server logs for any related/associated error messages? Sometime they can shed additional light on the nature of the problem.
Other than those possibilities, I'm not sure what to suggest. Unfortunately, custom PHP installs have a lot of potential for "borkage",and it is really hard to tell what might have gone wrong or where the actual problem might lie. I've no doubt that is one of the reasons (among others!) that DH will not support such installations - it would be a huge demand on their support resources.