There's no glitch as far as I know and I don't think cheats should have any effect on completion percentage. I got all 200 pigeons so I know they're all there, but before I got the last one I was missing one and thought of all the places that I could have possibly 'skimmed' i.e. not looked very hard because I thought I had already gotten it passing by before.
Have you checked the one in the little hole in the curved column at the airport? That's the one I missed and I was sure I got it before.
Maybe just try looking over the first few and last few pigeons on each island to make sure.
And btw, which guide did you use to find the pigeons?