This problem just got a whole lot more interesting. It attacked me, this morning.
Cleanini, and CHECKINI, did nothing to fix the problem, although CHECKINI did identify bad startup folders (the ones that were popping up).
What I did, was download the latest VLC2, from HOBBES. I extracted the ZIP file into a working directory. Then, I did a copy over top of the old VLC2. It replaced it as usual. Then, I rebooted, and I had the problem. In my case, it popped up a lot of folders containing *.mo files. Since I now know where this came from (VLC2, in my case). I deleted the whole directory, and ran cleanini, which cleaned that stuff out of the ini files. Next, I did a reboot, which had no problem.
Okay, I copied the same directory back in (there was no problem identified with the directory in the working directory, and it doesn't cause the popups). After reboot, the problem is back, so I deleted the VLC2 directory, and rebooted. No problem. I ran cleanini again, and it removed the VLC2 stuff.
I don't believe that VLC2 has a problem. It seems to be the copy that is causing it, but I need to do more testing. For now, VLC2 is not installed.
FTR, I did do cleanini yesterday, as part of my weekly backup.