This sounds similar to a problem I ran into when I first started playing with the program?
Are you using the PlayerTiles.bmp in beta assets? If so Make sure you aren't saving that over your GameObjectTiles.bmp in your graphics assets folder because they are different sizes and your player won't display properly. Instead in pixel editor create a new GameObjectTile.bmp and copy and paste the player sprites from PlayerTiles.bmp that way it will be the correct size and your player will display correctly. In any case your GameObjectTiles.bmp in graphics assets should always be 128x64 pixels