For some reason the option ''Choose start point closest to specific location'' isn't always working correctly in version 4.1.1.
I've read somewhere on the forum that another user also had this happen and that version 4.0.0 doesn't have this problem.
Sure enough, I have reinstalled that version and the seam alignment is as the setting should work.
Is there an update to the version 4 series as we were told? Then I hope this will get fixed, or else in V5