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
<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>