I was facing the same problems. In my case it helped when i cut all white area around the logo off. After that, with no margins around the logo, it always ended up on the spot i wanted to have it. Moreover, the size of the logo can be adjusted, and this may also be a possible source of error. If the logo is too big to fit on the right spot, the programm sometimes creates a mess as described above, especially if there is a lot of white area/margins around the logo...