One of the biggest mistakes that could be made in 0.85beta (from 0.9beta3 on I prevented it automatically) is to have selected “Remove Leading And Trailing Silence”. If the image file contains silence at the beginning (e.g. 1 second) it will be removed and everything get moved by one second. So you should deactivate this option for 0.85b4. If this is not the problem, try a different gap detection mode and compare the generated CUE sheets manually.