The issue isn't just pear; a lot of common php apps - Tikiwiki; PostNuke; Drupal; b2evolution etc, which ship with their own versions of the xmlrpc(s).inc files.
Affected programs will need updating. The fix I'm using, is to grep all xmlrpc*.inc files for eval('$m->addParam(' . $_xh[$parser]['params'][$i]. ");"); and then overwrite the effected xmlrpc.inc and xmlrpcs.inc files with the updated ones, across the board.
--HV
More investigation found that --with-xmlrpc is not effected
