using v1.90 + paypal standard (business account)

Have strange issue where some orders go through with payments no problem while some orders come through in admin as complete but no payment is taken in paypal!? If there was a problem with my configuration of paypal/PDT/IPN wouldn't if affect ALL orders? Can you recommend a solution/troubleshooting steps?
Thanks.

ps plan to upgrade to 2.5 but need to solve this for current site. thanks.