exactly i think this may be limited to the specific raw filesJust a suggestion... I too sometimes want to add a few secs of black segment when my edited video starts abruptly and it often didn't work when VRD joined the video.
I finally cut a 30 sec segment from a video that started with the 5-10 secs of black/no volume frames I wanted - whatever else came after didn't matter as I wouldn't be using it.
Then I recoded that segment in different resolutions (1080, 720, SD) and audio types (AC3, AAC, 2ch, 6ch)
Now, when I need some black padding, I load the "Black" file with resolution and audio that match into VRD, mark out a length of black I want for padding and add that segment to the Joiner queue with the rest of the segments from the main video I'm working on. I have had no further problems with joining opening black to programs.
My theory is VRD Joiner can't properly sync a file as short as 5-10 sec, especially if the short segment needs recoding to match the larger video.
Creating 30 sec files and cutting from the matching type allows VRD enough info to do a proper sync. Bluestacks Kodi Lucky Patcher
This may be limited to the specific raw files I create with my Hauppauge HD-PVR, but worth a try on your files.