A Pokemon's "Shiny" status is directly generated by the PID# and nothing else about the Pokemon will affect whether or not your Pokemon is shiny. All it means is the PID that Pokegen auto-generated for your Pokemon was not a shiny PID.
In order for you to get a "Shiny PID" certain things must be entered.
1. Under tab 5 (OT/Misc) you must insure that the 2 ID numbers are correct. The first # is your Trainer ID (TID) which can be found on your trainer card in-game. The 2nd # is your Secret (SID) which can't be obtained via normal means. To get your Secret ID I recommend using Pokecheck.org which is a GTS Legality checker. Follow the instruction there to upload a Pokemon you caught or bred (not traded for) in your game (this is not an actual upload, just a data copy, the Pokemon never leaves your game) and you will see your SID.
2. Under tab 1 (Main) next to the PID Line click the 'F' button
3. Fill in the relevant info (IV's [0-31], species, Nature, Gender, ability) and ensure that the 'Shiny' box has a check in it.
4. Click 'Search' and select the PID you wish to use.
That's the Pokegen way to get a PID. Personally to get a PID I use a program called RNGReporter which is used by people who, instead of 'hacking' their Pokemon with Pokegen, prefer a method called 'RNG abuse' that uses a program (RNGReporter for Windows, I forget what the MAC Equivalent is) to determine what time they need to set there DS's clock to in order to predetermine the Stats, Nature, Gender, Ability, and Shiny a Pokemon has when they catch, hatch, or receive it from a Wonder Card. Setting up your RNGReporter can take a bit, and still requires you have your TID/SID, but it can generate PID's (though they need to be converted from Heximal to Decimal) while giving a much more accurate ability to Specify all the aforementioned qualities of your pokemon.
It's very easy for an amateur to make a mistake with Pokegen and find that the Pokemon they made does not pass a legality check. If you are patient (it can take a couple days to really learn the system) RNG abuse produces 100% legal Pokemon because all you are changing is the time on your DS, not introducing or altering data to the game. Normally I RNG my pokemon, I only use Pokegen when I want to have a specific move set that would require multiple generations of breeding and am feeling lazy.
Hope this helps you get your shiny Pokemon generated.