I'm working with the NPI database
What is "the NPI database"?
But the FileMaker Pro 12 is only opening about 500,000 of the points. It's in comma separated values format
Do you mean that you are importing data from a CSV file and only about 500,000 records are importing?
If so, there's an upper limit on how large a CSV file can be imported into FileMaker. You'll have to break your large CSV file into smaller files and import from each in turn to get this data into FileMaker.
For More Information see: Import of a large CSV file halts after 4GB
This is one of many acknowledged bugs that can be found in the Known Bug List thread here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: https://www.dropbox.com/s/jt09b82i0xijbu3/FMP%20Bugs.zip