I have limited experience with FCP so I am sorry to take up your time with this question.
I already have one project on the go which when I preview looks fine, the image is as it should be and each clip of the movie plays through successfully.
I have just opened a new tab to make a new edit of the same material, and when i cut and paste clips from the old to the new tab and play them back, the image pulses every few seconds. Different clips pulse to a different degree. Have just rendered all, and some of the clips are still pulsing every other second. Its only slight, but definitely doesn't happen on the other edit...
It sounds like maybe the sequence settings might be different. Instead of making a new sequence just copy/paste (select sequence - command C - command V) and rename. Then start your new edit on the renamed sequence.
FCP Studio 2
Dual 3Gg Quad Core