I had the 999 bug when I first completed this. After beating the end boss I then went on to try and collect the rest of the light seeds but quickly found that my overall tally was one shy of the achievement even tho it said I had 45/45 for each part of the game world. I went to last place I collected some light seeds but to no avail.
The oldest save I had from the game had me at 272 light seeds and when I did the math the amount I needed added up correctly so I just played on again from there. After I had cleared each area of light seeds I checked my map to make sure that the math was still correct and eventually I found myself with the full 1000 needing just that final one at the end of the game.
I have no idea what caused the 'glitch' or 'bug'. The only advice I can give to anyone who wants the Light Seeds Master achievement is to check your in game map regularly to make sure that the amount the game says you have and the amount it says you need still add up correctly.
