Edit: It seems the problem is the format of the video file, Inter-frame and stuff, as converting it to an image sequence works perfectly (but awfully slow), I will try to convert it to another codec and report. Report: Apparently using intra-frame format makes the file big and slow as hell, same as image sequence. But at least it works.
I'm learning about motion tracking, and I'm having a weird problem. In the movie clip editor, the video is kind of stuttering and jumpy. At some frame it would freeze for 3 or 4 frames then continue, but skipping those frames ( sometimes continuing from the frame it stopped, or jumping back, resulting in the video losing some frames and becoming a complete wreckage ), while the trackers would act as if there was no stutter at all (their motions match the motion in the original video). All other video players haven't this problem. Using another program and played frame by frame aside each other, Blender is completely out of sync with the original.
An interesting thing is that when I reload and prefetch the clip again, the problem is gone, the clip plays smoothly and the trackers match up nicely, but after some time of working, it returns, and it always does when rendered.
This happens at many points in my clip, and when rendered the 3D objects seem to be out of sync with the video. I have tried rendering the 3D elements as transparent and later putting in on the video, and it works much nicer. Any help will be appreciated.