In MPC-HC go into settings then Player -> User Interface and under "Seekbar Hover" turn on "Show Video Preview"
Close settings and right click on your video screen and go to View -> On Top -> While Playing Video
Exit out of MPC-HC entirely
Find a video file and "open with" MPC-HC (or just double click it if you already have as default association)
Without pausing the video move your mouse over the player seek bar and the preview box shows up behind the MPC-HC window

After pausing the video the behavior works as expected

You can resume playback and change video files and the preview window will not go behind the player until you close out entirely and go back in.
It may take a few attempts to replicate the bug, it doesn't always trigger. I find if you close and reopen MPC-HC 2-3 times it should occur, maybe some race condition with how fast the playback of the video begins playing (you could try Always On-Top rather than just While Playing Video?)
In MPC-HC go into settings then Player -> User Interface and under "Seekbar Hover" turn on "Show Video Preview"
Close settings and right click on your video screen and go to View -> On Top -> While Playing Video
Exit out of MPC-HC entirely
Find a video file and "open with" MPC-HC (or just double click it if you already have as default association)
Without pausing the video move your mouse over the player seek bar and the preview box shows up behind the MPC-HC window

After pausing the video the behavior works as expected

You can resume playback and change video files and the preview window will not go behind the player until you close out entirely and go back in.
It may take a few attempts to replicate the bug, it doesn't always trigger. I find if you close and reopen MPC-HC 2-3 times it should occur, maybe some race condition with how fast the playback of the video begins playing (you could try Always On-Top rather than just While Playing Video?)