While you inspected the code you could found the "seqname_format"
option:
$options = array('persistent' => true, 'seqname_format' => '%s');
// by default 'seq_format' is '%s_seq'
$db = DB::connect($dns, $options);
This is not available in my version (came with PHP 4.1.2) or I can't seem to grep it from the sources.
Since the PEAR installer is not yet production quality, I always use bundled versions of PEAR because it is easier to tell my clients to upgrade PHP (along comes bundled PEAR) than to trouble them with the buggy PEAR installer.
Thanks and cheers
Roko