Duplicating files, even after deletion

I have a persisting file/folder problem. The problem exists on both my OS resident SSD and the internal standard drive - and between them.

On my C drive, there are folders that contain empty other folders. I have tried to delete the empties - many many times and they keep coming back - even after emptying the recycle bin and rebooting. Even after running Ccleaner and wiping my free drive space... and rebooting again.
On my other drive it happens also.

The reappearance happens when I access these folders from a graphics program.. photoshop, sketchup, paint.. etc

To make it even more fun, some of the folders on C are also on G (the other internal drive) as backup.
This duplication, reappearance of empty file folders happens on both drives as if the main folders are linked.

Last week this other drive was partitioned and in a last ditch effort, I backed it up on a brand new external drive and reformatted it. It's no longer partitioned.

This behavior persists, even after a reformat of the drive that does not contain my OS.

Might someone know how to make these deleted empty folders, stay deleted?

I don't have any connected devices. I only plug in the printer USB when I want to print... which is fairly rare.
My start up list - I just looked it over and I'm not entirely sure what all the windows start up features do but they do not say anything folders or auto backup.

Thanks you two

msconfig shows 4 programs.. only one is checked.. my AV
the others are adobe reader (twice) and
realtek HD audio manager
in Ccleaner, I did find two additional tasks that belong to non OS software and turned them off (adobe updater which should have been turned off to begin with and one sketchup task) and there are a few belonging to my graphics card (nvidia stuff) that I don't think I should turn off.

I have not rebooted yet.
Interesting to note that the duplication happened even after a reformat of that one HD to a folder that didn't exist a week or so ago.

I don't use libraries.. but I checked them - there's nothing in them that didn't come with the OS
I'll dig into the process monitor tomorrow.

I'm shutting down for the night.. will check things in the morning.

again.. thanks. I'll let you know how it goes

Hello opal -

Here is your clue: "the reappearance happens when I access these folders from a graphics program.. photoshop, sketchup, paint.. etc"

The graphics programs are most likely creating what is refered to as a "scratch disk" - this is normal and required by almost all graphics programs.

If it really bothers you, go into each program's Preferences settings to see how you can control the location and size of those folders. However, in order to run the applications you will need those scratch discs (folders).

Regards,
GEWB

Well.. I've been messing around with this stuff all afternoon. I think I got photoshop's scratch disc issue squared away but sketchup is making me nuts with it's materials files. I set it to default to one folder.. files just appear in another - on the other hard drive, I close the program, delete the empty file folders..empty the recycle bin, reboot and try again. I've even gone into security settings to disallow the system access to the materials folder (rendering the already cruddy windows 7 search even more useless).
I have yet to mess with paint, gimp and a couple others

My bad.. I've been blaming windows 7 for this and it does look like it's the other software causing it.

oh.. it doesn't just happen on boot.. I can have a folder open after I delete stuff.. access the folder through the graphics program and poof.. they're back! poltergeist on my machine