Insights ... maybe not ... cause haven't experienced it. Did try to find something in Tracker ... no luck there. So this is more places to look and things to check.
Should you be worried about it ... well, you say you are able to finally get a restore ... but, if there is an issue might be best to investigate and know for sure rather than let it fester and possibly get worse. My 2 cents of course.
So ... here are some questions for your research and places to look, etc..
You have debug output .... which doesn't appear to help, but ....
In the courses that fail, what mods/blocks/theme etc. do they contain that other courses may not have? Any addon plugins?
Are the plugins up to date ... any needing an update?
In moodledata/temp/backup/ the directory used to build backups, are there:
1. any .log files of size larger than 0? If so, they are ascii text, so see what's in them. Clues maybe.
2. any folders by contenthash name ... bunch of letters and numbers. Go into one of those and see what's in there ... should find xml files that are like roadmaps to the folders contained there in ... files.xml relates to files directory, etc. Is there a moodle_backup.xml present? Thatf's the main roadmap for a backup. Is there an .mbz file present by the name backup.mbz?
How about other server logs? Web service error logs ... see 'MySQL has gone aways ...' or other entries which might provide a clue?
Are the courses about the same size ... ie, the .mbz file?
Are there any php_error files in directories of code? PHP setup and the way you are running your site there could be error logs in directories where failure occurs. In backup directory of code?
Got moosh installed? If so have you tried restoring using moosh?
How about backups from the command line? /moodlecode/admin/cli/ there is a backup.php script that will backup a course by the backup preferences in site admin menu and put those backups in a directory other than moodledata/filedir. Plus CLI script takes your web service out of the loop. Suggest trying a CLI backup of one of those troubled courses to see if that works without error.
'spirit of sharing', Ken