I'm a little confused about how Bank decides which Pokémon are ok to transfer and which ones aren't. I have no idea why my Dusknoir and Togekiss were unable to be transferred. The Togekiss was hatched from an egg that Champion Cynthia gave me and the Dusknoir was caught on route 209 as a Duskull and evolved, both from my Platinum. I decided to evolve an extra Togetic I had and I used the nontransferable Dusknoir to hatch a new Duskull and evolve it all the way up to another Dusknoir and those two don't have a problem transferring.
Edit: Just out of curiosity, I decided to dust off my action replay. I've got a bunch of codes that alter your Pokemon when you mark it on the PC. I took a Ditto that I caught in a hidden grotto and made 6 clones of it. Clone 1 I left as is. Clone 2 got maxed IVs. Clone 3 turned shiny. Clone 4 got a nature change. Clone 5 got the pokerus. Clone 6 got maxed IVs, turned shiny, got Pokerus and got the nature change. All 6 of them were able to be transferred into Bank (Don't worry, I didn't go through with the transfer), but that original Dusknoir, who was also sitting in the box with the 6 Ditto clones, was still not able to go through. I don't know what that filter is looking for but it clearly isn't looking in the right place. I'm actually pretty irritated by this.
Edit 2: Also, I just found out that if you change the group your boxes are in and then move them back to the first group, it doesn't put them back in the original order. My boxes were starting from 27 and ending with "98, 100, 25, 26, 99, Transport Box" in that order (boxes 1-24 are in Group 2, now titled 'National Dex'). I managed to get the order to go "27, 28, ..., 98, 99, 100, 25, 26, Transport Box" by moving those last 3 and putting them back in Group 1 in order, but there is no way to get 25 and 26 back at the front without either renaming all of the boxes or moving all of the boxes and moving them back in order. And it's not like it's easy to move a lot of boxes at the same time. Every time you register a box to a different group, it jumps you to that group and you have to switch groups to register the next box. That is a real OCD mess and I'm afraid I may eventually go through and renumber all 76 boxes. But when I say it like that it sounds like too much work and now I don't care enough to do it.