Thank you for posting your experience with this common problem. I would like to get a better understanding of your specific experience so I can pass on the correct information to our development team.
Are you currently using Pix4Dcapture on an iOS or Android device? As my colleague, Andrew pointed out above, there are different types of flight lines in your automated mission. There are solid white lines which are referred to as capture lines and dashed white lines that your drone will take between capture lines, these are referred to as transition lines.
From my understanding, your drone is flying at a 45-degree angle throughout the entirety of the flight, not just on transitional lines. Is your drone flying in a different manner on these separate lines? Does your drone also fly in this skewed orientation when utilizing other mission types (single or double-grid)?
Ensure that you have the latest firmware installed on your drone and that you are using the latest version of Pix4Dcapture.
Best,
Josh