[I agree with what the others above have said... but...]
You seem to be implying that the cause has something to do with the floor vs. the hand corker, right? IF IT DOES then it could be that you have your hand corker setting the corks deeper into the bottles than the floor corker; you haven't noticed the same thing happening because those hand set corks simply did not rise above the bottle top.
Perhaps another possibility... if the floor corker is to be blamed (I personally don't believe it is the problem), is that the floor corker is compressing the cork more than the hand corker and something about the nature of the corks you're using allows them to recover more fully from the hand corker compression.