Justification for IPv4 these days is becoming the norm. Our providers except for one ask us for valid IP justification when we order more. Bring on IPv6!
I've never had this issue using WHMCS. If you have SSH access on the server, you might want to check the Apache logs to see if you can catch the culprit.
Are you running any other scripts on the same hosting account?
If you want to use Moneybookers for WHMCS, you will need a Moneybookers Merchant Account first. So you'll need to contact Moneybookers about that. WHMCS fully supports PayPal.
Will adding >/dev/null 2>&1 onto the end of cron.php stop cron emails being sent at all?
Example
php -q /home/username/public_html/domain.com/billing/admin/cron.php >/dev/null 2>&1