Reddit will only show comments from subs that aren't private. OP deleted those public comments but the ones in private subs weren't displayed for him to delete manually.

Later when those subs became public, Reddit then displayed those comments. OP never manually deleted those comments because Reddit never displayed then to him in the first place.

Specific for OP, /r/JavaScript for example, was private when OP manually deleted his comments on June 24th. It just came back up this weekend. Thus why all OP's /r/JavaScript comments are now visible in this video. If you pause and slowdown the video, notice that all the content is from /r/JavaScript and /r/techsupportgore (which also recently came back online.)

Users (reasonably) assume that what is listed on your profile's submsisions/comments is everything. But it isn't. It's only the last 1000 entries in the database, and it doesn't include content in private subs, or blocked users (which I've read but can't verify), and maybe some other scenarios. But the big one, especially for right now, is privated subs.

It's pretty arguable though that Reddit should be showing all the content you made, even in private subs you no longer have access to. Could be technical or corner-case abuse scenarios driving this restriction. (Even if that's the case, it'd be nice if there was clearer communication to users about what is and isn't included in your submission/comments listing.)

I guess all the people in the comment thread who said it solved their problem as well are full of shit too

Or you're just doing something wrong and haven't figured it out yet/can't admit it