A normal rescan compares the last modified timestamp on disk with the timestamp recorded in the database. If the file on disk has not changed, it is not rescanned.
Since this fixed the problem, the real problem is lurking in the initial process of adding files.
Can you please try the following to help me find the issue:
Select one of the folders with the problem (the one with the most files is best) in the Media & Folders View.
Right-click and choose Remove from Database... to remove the folder from the database without deleting it from disk.
Restart IMatch.
Then add the folder again.
If some of the thumbnails are again black, please attach the zipped log file (Help menu > Support > Copy Application Log File) or send it to my support address (see below) and include a link to this post. The log file may tell me what errors IMatch is experiencing when adding the files. I guess it is a 'stress' issue.