I just looked at the Nassau County Repeater list, and it looks like there isn't any Tone Out information for any of the repeaters in Nassau, just tone In. I'm not sure why the values are being flipped or not included with the CSV dump file. (I didn't check to verify)
Have you tried using
RepeaterBook.com to build your CSV files? I use theirs for programing my ham radios and just finished programming a new Anytone 878 this week using their CSV downloads.
Tone Out isn't always shown on ham repeaters in the RRDB (or RepeaterBook, for that matter). Frequently submissions come in which don't specify whether the submitted tone is input only, or both input and output; when an admin asks for clarification, a typical response has been "that's the tone to get in" and the submitter doesn't know if it's transmitted. In addition, for whatever reason some repeater trustees don't transmit the PL tone.
If the repeaters in Nassau all use PL for both transmit and receive, by all means submit that so the RRDB can be updated.
I've been working on an updated ICS-217 form for Ohio ham radio repeaters using the RRDB and RepeaterBook as my starting point, then verifying each repeater as I travel around the state; I'm finding that quite a few frequencies are listed in RepeaterBook which either don't exist or are a different format than what's listed. A big part of the problem is clubs which took advantage of the "bargain" when Yaesu was dumping Fusion repeaters on the market at $500 a pop; they're now either Fusion only or are dual-mode, but the changes were never submitted to online databases.
I won't even get into how insane it was for groups to trash perfectly functioning 100 watt GE Mastr II or Motorola Micor repeaters in favor of the Fusion repeaters, which can't do more than about 10 watts continuous duty without burning up.
Update: Just for giggles I downloaded the local CSV file of all identified frequencies, and it only shows Tone Out, not Tone In. Never noticed it before as I usually copy and paste only what I need directly from the web page into a spreadsheet, edit that and create a CSV from it. I'll have to see if that can be changed for the ham frequencies.
To the OP: what radio and software are you using? I recently was building a codeplug for my ID52A and had no end of trouble importing a clean CSV file into the Icom software.