Okay, I've made a video for my son's hockey team. I used the fast dissolve transition inbetween each clip.
As the movie plays you can see when the transition is about to happen cause the picture gets a blurr/faded look to it. Once the transition happens the new clip stays blurred/fadded for about 1-2 seconds and "pops" to the nice clear clip that it is. I've tried taking out the transitions but it still does it. Any idea what might be causing the clips to fade like this?

That's typically a video card issue that causes that. Usually onboard video chips and Nvidia cards seem to be the worst culprit. You can try updating the drivers for you video card/chip (from the manuf site like Nvidia, ATI, etc), update directx from Microsoft (not thru auto updates, have to do it manually thru their site).

If those don't help, then in MyDVD or videowave, go to Tools -> Options and set the encoding to Software instead of Hardware.