Not so much a solution, but a little encouragement to those who are stuck with the 999 light seed glitch. I viewed all of the posted solution yet none of them mentioned anything about how to "avoid" or if there is a fix to the glitch.
My finding: the glitch is not avoidable, per se, and if you are lucky, you might not encounter said glitch. However, this does not PREVENT you from completing the light seed achievements! A HUGE tip I could offer to those who are now starting the game is to do your best to keep track of which light seed you are able to get and follow the video guides provided on TA's walkthrough. Keep track of how many seeds you have gathered according to the back button map and if they tally up to the total light seeds correctly. If not, save your game, reload a previous save file and see if the total number is still incorrect or not. This will help you pinpoint the precise moment the glitch occurred and thus, which stage is glitched and to resume searching that area for all of the light seeds available.
For example, take into consideration the stage "City Gate" of the "City of Light" series. This stage is available from the beginning of the game after you finish the first stage. Right away, you are able to get 40/45 light seeds available on that particular stage without using any Ormazd plates. There is 1 Blue Ormazd plate on that stage that will help you get 5 light seeds. Now, after comparing a couple of my save files, I realized my "City Gate" stage was listed 41/45. Glitched stage found! However, I wasn't able to pinpoint which seed caused the glitch if there was even a glitched seed. I proceeded to gather the 5 seeds from the blue plate and lo and behold:
46/45 City Gate...
So be vigilant in your search for the seeds. You may have encountered a similar glitch to mine, which does not prevent you from missing the achievement, but is a pain in the arse to find that missing seed. Save often and keep on searching!