I found a way to systematically reproduce this, using attached project.
Open SE with default config (-sc <empty_dir>), using an empty dir seems critical for reproducing, don't use a default config that already exists.
Open attached workspace: prj.vpw
In smart open, double click on the grandparent directory of prj.vpw (the parent of mainprj)
Type "main.cc" in smartopen to show all the main.cc files
Right click on the column headings and enable "Date Modified"
Notice that all dates are 12:00 AM
I did this on a Linux x64 Centos 7.2 machine, but maybe only Linux x64 needed? If centos needed, can use my VM (but need to install beta3) as instructed here:
https://community.slickedit.com/index.php/topic,15458.msg58927.html#msg58927