Make sure that whenver you change IVs, EVs, Natures that you click the stats tab and click stats max. But that is not the true culprit. It is your IV selection. When you go to choose a PID for non hatched pokemon you can only use type 1 PIDs. Boss had a type 7 PID and Tidus had a type 3. You will have to play around with the IVs until you get a PID/Nature IV combination that suits you. You can also use http://projectpokemon.org/editing/pidivgenerator.php but I have trouble using it myself sometimes. Heres the pokemon with the changes I made, It changed Tidus to a girl, I don;t know if this matters or not, but if it does, then you will have to mess around with it more.
P.S. PBR is a bad checker. If you want a real test to see if your pokemon is fine or not, use the VS recorder and try and upload a video of said pokemon.
tidus test.pkm
Boss.pkm