With limited information about the theme customization, settings, and pricing details, this is almost impossible to solve. As more information is given, I'll continue to append updates. Here's where I would start:
What do inserted prices look like? Do you insert prices with 4 significant digits after decimal in backend? Are you seeing only two in frontend?
Do you know if there is custom code applied to prices in the frontend templates that use rounding functionality directly from PHP instead of magento wrappers?
Create a temporary script in root directory with this, but change the ID to a product that is showing the improper price:
error_reporting(E_ALL | E_STRICT);
$mageFilename = 'app/Mage.php';
$id = 1234;
$_product = Mage::getModel('catalog/product')->load($id);
Post the relevant output data. This could help identify the next direction to take. We want to determine if the correct data is returned and what it looks like. We can then start to target overriding functions, perhaps
getFinalPrice(), or if there are custom rounding crap being done prior to function calls to obtain pricing data.