Example: if you import products with different prices for 2 additional websites, so you have 3 lines per product in CSV and you have more than 33 products, at least one of them will have “empty”/zero price on default website.

The problem is caused by splitting your file into batches in Magento core, batches of 100. A good thing is that a batch size is taken from a configuration and can be easily replaced with a value which will fit your needs. For example, for 3 lines per products can be used any value which can be divided by 3, so the nearest to 100 is 99.

Just add this lines to your module config.xml or app/etc/config.xml

<default>
    <general> 
        <file> 
            <!-- Because we have 3 lines per product it's important to have $bunch_size % 3 == 0 --> 
            <bunch_size>99</bunch_size> 
        </file> 
    </general> 
</default>

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