I've been having a problem with tmk for a while.
I did find some nice pokes with T-search, but it didn't seem to matter how I pasted them, tried all sort of things. My trainer just wouldn't work.
Next thing I did was download another TMK, which seemed to be the same, only the box was a different color and this one seems to work the way it should.
I'm not really sure if this is the problem you encounter..