For some reason my custom filters are not working properly. Whats happening is when I want to sort a collection or other group of images and I pick 'flagged' or 'rated' it does not automatically sort the images to that. The only thing I did recently was delete a few old collections to streamline my collections. Would that have caused the issue?
Perhaps if you posted a full-resolution screenshot of the entire LR window, that would give clues as to what's going on. (Deleting a few old collections shouldn't have made any difference.)