Thanks everyone for the responses. I have tried adding control points before alignment, and this is weird… The place where I put the control points, and I literally only put 2 for about 20 frames, now aligns perfectly as if there was no issue, but now it has split elsewhere at a point that was previously aligning fine… Why could this be… Its as if the program thinks it has to split it up and the control points have told the program not at that particular point…
This must be a settings problem, these are my settings