I'm having the exact same problem. Interestingly, other emails DO arrive. For example, s2member sends us a notification when a new user registers or purchases. The only email that goes missing is the new user registration email that users should get with their user name and password. It's a pretty big problem for us right now.
Here's my log in case it helps.
WordPress® v3.2.1 :: s2Member® v110815 :: s2Member® Pro v110815
Memory 47.07 MB :: Real Memory 47.25 MB :: Peak Memory 47.10 MB :: Real Peak Memory 47.25 MB
www.streetofwalls.com/?s2member_paypal_ ... eturn_url=User-Agent: WordPress/3.2.1;
https://www.streetofwalls.comarray (
'txn_type' => 'web_accept',
'txn_id' => '51E81099V98377422',
'custom' => 'www.streetofwalls.com|0',
'invoice' => '4e6a132ebbf58~98.124.134.5',
'mc_gross' => '1.00',
'mc_currency' => 'USD',
'tax' => '0.00',
'payer_email' =>
'xxxxxx@gmail.com',
'first_name' => 'xxxxxx',
'last_name' => 'xxxxxx',
'option_name1' => 'Originating Domain',
'option_selection1' => 'www.streetofwalls.com',
'option_name2' => 'Customer IP Address',
'option_selection2' => '98.124.134.5',
'item_name' => 'Purchase Merger Model:',
'item_number' => 'sp:1176:4380',
'proxy_verified' => 'paypal',
's2member_log' =>
array (
0 => 'IPN received on: Fri Sep 9, 2011 1:22:58 pm UTC',
1 => 's2Member POST vars verified with a Proxy Key',
2 => 's2Member originating domain ( `$_SERVER["HTTP_HOST"]` ) validated.',
3 => 's2Member `txn_type` identified as ( `web_accept` ) for Specific Post/Page Access.',
4 => 'Specific Post/Page Confirmation Email sent to: "xxxxxxxx" <xxxxxxxx@gmail.com>.',
5 => 'Specific Post/Page ~ Sale Notification URLs have been processed.',
6 => 'Specific Post/Page ~ Sale Notification Emails have been processed.',
7 => 'Storing Specific Post/Page Tracking Codes into a Transient Queue. These will be processed on-site.',
),
'subscr_gateway' => 'paypal',
'hours' => '4380',
'sp_ids' => '1176',
'ip' => '98.124.134.5',
's2member_paypal_proxy' => 'paypal',
's2member_paypal_proxy_use' => 'pro-emails',
's2member_paypal_proxy_verification' => 'xxxxxxxxxx',
)