So many people I talk to are shocked to find out that new stones aren't flat out of the box. I know this sucks but it's the truth, you need to flatten all of your stones before using them.
New stones can come with stickers on the surface (which when removed leave glue behind) or maybe just ink imbedded into the surface due to fancy markings, often come uneven, all come with high edges/corners, and some will even have a sort of surface crust on them that needs removing before the stone actually works correctly.
My advice is to soak (if your stone requires soaking) the stone first and then follow with rounding the edges and ends, then flatten, then round the edges and ends (again). The order that you do this procedure is the same that you do for flattening a stone each and everytime although it's much more important to do the edge rounding at the pre-flattening stage when the stone is new because these high edges won't allow for you to flatten the stone correctly because the flattening stone/plate will be lifted off of the stone's surface. Sounds crazy I know - but trust me this is key to getting your new stone(s) really flat.