It appears that every product is indexed, I cross-checked the published products and the count of the indexed, and it’s matching. The counter of non-indexed items has a known bug, it’s not working correctly in some cases.
I was able to re-create this issue on my test environment, and I have found the source as well. This happened when a product was saved after the index was created. Everything was refreshed in the index, except the custom fields. So when you saved a product the custom fields data was not re-indexed.
I have solved the problem by slightly editing 2 files in the search plugin directory and re-created the index for you. It should display the results correctly now.
I will include this fix in the upcoming update of course, so you don’t have to worry about the modification getting lost once you update.Best,
If you like my products, don't forget to rate them on codecanyon :)