Make sure when you make a clip you set a key at the beginning of the clip and at the end of your clip.
Also you need to also make sure that there are no other keys on your charater when you apply the clip.
It's easier to have a body control for your character that selects all of your characters controls. That way your positive you're keying everything when making the clip.
It's easier to only apply 1clip at a time for your animations. If you have more than one clip then make sure the keys match up between the clips and that none of the clips are overlapping.
Just some basic pointers about making clips. I hope this helps.