Haha Andre you found me (I am really a fan of sci-fi stories).
I found that full rescan time has increased significantly, especially when there's a folder (Movies folder) with a 30 or more videos selected.
And looks like during first rescan, although I am seeing music files, their album art isn't being loaded for some reason. The problem is fixed when I unselected Movies folder, force stopped PA, and relaunched it again. Rescan is very quick after that and the album arts loaded. It looks to me that Poweramp is taking more time than usual scanning video files.
Now on to the main problem, I am still seeing mkv files in Poweramp but they are treated as mkv (not mka like it used to), which is kind of improvement I guess, but doesn't really fix my problem..... I am not entirely sure why my test result contradicts with yours but have you tried with this test file? https://github.com/Matroska-Org/matroska-test-files/raw/master/test_files/test5.mkv
Update: after the rescan is completed, mkv files disappear from PA recently added list as I enabled Ignore video tracks... But I am still seeing two above bugs.