I have found out why! It was strange to me that the numbers were correct in terms of the indexed documents and the SKUs, so I suspected that it might be some kind of exclusion.
The problem is that you have a post date inclusion rule configured to include results from date 2014-08-01 to 2034-08-01. I've checked, and all of the not working SKUs are before the given date range. I have disabled this option on the Advanced Options -> Exlude results panel, now it search through all the results.
However one thing will not work for sure yet with the index table engine, and it's the product SKUs with the forward and backslash “/”, “\” characters. So “NOZZLEFJ3/4HH-4.0” might not return anything. The good news is that it will work with the regular engine, and I'm going to add support for more special characters including the slashes for the upcoming version.
It's a security related concern, and I want to carefully test it to make sure that it's not something that could be used for hacking the database of my customers.
If you like my products, don't forget to rate them on codecanyon :)