Sorry but I'm not sure what a "capture scratch mpeg" refers to. What is the source clip format? Sequence settings used?
I've had experienced in the past similar to yours, such as the muzzle flash from a gun disappearing. This was with interlaced footage - the flash was so brief that it was only found one ONE FIELD of the video FRAME, so I could not pause on it, would only see the field without the flash.
In the tools menu of the Program Monitor, you can tell it to display BOTH fields, or UPPER or LOWER.
I tried watching your YouTube video, but without audio, was not clear on what I was supposed to see. Please clarify the issue and include details of the footage type and sequence settings used. If for example you put a 30p clip into a 24p sequence, all 30 frames are not going to get played, some will get dropped/skipped to get 30 frames per second down to 24 so maybe something like that is going on and you're missing the lightning flash?
EDIT: Was footage captured from tape? If so, how?
Thanks
Jeff Pulera
Safe Harbor