MiserablePileOfSecrets

I've found a few shiny pokemon in my game thus far and managed to catch them, however only one has counted towards the achievement. All of the ones that didn't count towards my total were found in double wild battles when travelling with a partner, while the Kricketot was found while I was alone and the only one to count thus far.

So I personally like playing in the smallest window for the game but after one time of playing on medium size, saving and eventually closing and reopening the game I can't go back to the smallest setting, however the large and fullscreen options still work. Is there a way to fix this?