That's just an inherent problem with checkouts going through PayPal's site (such as PayPal Pro Express Checkout), as they do not automatically redirect the buyer to a post-checkout thank-you page where GA tracking code could be triggered to track the conversion. If you are not selling downloads, the buyer has no incentive to load the thank-you page at any point (where we normally provide download links), so those conversions may never get tracked.
Google Checkout can transmit conversion data to Google E-commerce Tracking and thence to Analytics directly via their backend even though they also do not auto-redirect the buyer to a thank-you page, and we can auto-redirect buyers who pay directly with a credit card using either Authorize.Net or PayPal Pro Direct Payment.
If you want reliable, consistent conversion tracking, you would simply need to give up on accepting PayPal at all, and only accept Google Checkout or direct card-based payments via Authorize.Net.
More information about how tracking works and what factors can interfere with it are discussed on this FAQ page: