Thank you Peter much appreciated. I tested it again and I have noticed it overwrites my projection in the Map Options window from British National Grid (1mm accuracy) [EPSG:27700] to Longitude / Latitude (WGS 84) [EPSG: 4326]. When I change the Map Options back to British National Grid the cut data looks fine and just the cookie boundary is skewed. No idea what causes the cookie/boundary to be changed to Longitude / Latitude projection, double checked and created a new boundary ensuring the Map Options projection was British National Grid when I digitised it but same thing happens. It is however cutting the data correctly.