Ok. I am not sure if this was intended, a limitation of the program, or a bug. But I will try my best to explain.
I have example A that I simply want to extract and train so that I can replace example B with A. From what I understood, all I need to worry about for A is simply to make sure that the alignments are fixed using the Manual Tool.
I take a small video, extract it at 5 frames interval. Then Tools->Manual, I select the generated alignment file and select that video again and hit Manual. It loads, and the bottom thumbnails actually show everything accurately and correctly. Even if I enable the mesh overlay (F9), they are all aligned perfectly. However, it is when I click on any of them that the alignment severely jumps WAAAYY off. And when I iterate through all of them, they end up being very misaligned, but only if I view them in manual mode. If I don't touch them, they are fine. Now this happens for any video or any image set, on all the frames except the first one.
In one video, there are several scene changes of the environment. When I view them in the manual tool, they are all there and aligned perfectly. But when I click on them, not only do they misalign, but the image actually changes!
After some tinkering, I found out what the issue was. It appears that skipping frames doesn't play well with the manual tool. If I extract the entire video frame-by-frame, the manual tool shows correctly even if I iterate through the images. So here is the behavior that it has: If you extract a 400 frame video at 5 Frame interval yielding you 80 frames, and then launch Manual Tool, the manual tool will first display the correct frames. But when you press play, or click on any of them or just hold down X to iterate through them, they all get "misaligned", but in reality I don't think they do, I think that the manual tool will display the video frame-by-frame regardless. So if you view your extract frame 100, the manual tool will show you frame 20 of the video with the alignment set for 100!
Now I don't know if I am doing something wrong here, or missed something. I can't seem to find any answers, so I'm posting it here. Can someone help me figure this out? Or is this really something wrong? Just to be sure, I updated the app, and still gives me the same behavior.