Manually setting keyframes resultes in damaged videos?

[Dominator]

I added some keyframes in the log-file GordianKnot/VirtualDub creates after the first pass (by replacing intra 0/2 with intra 1). When using bi-directional enc. it sometimes ignores the keyframes I inserted. But even when it works, for example without bi-directional enc. and the keyframes are in the video, there are black or white "blocks" in the video, which wouldn't be there if i didn't insert keyframes.

How to insert keyframes properly?

Thanks in advance