Ok so I looked through all the posts like this and it didn't answer so here it is.
After installing a new theme I know the folders get rearranged and I have to reorganize them, no biggie. After installing a theme today (DC7 Centered) on my Bold 9700 they all were unorganized as usual. I used themes before and even this one before. But this time it just threw all the icons (including some that didn't seem to make sense [Bluetooth option that looked like a wrench, never seen that before]) all in the same folder. There wasn't even a Home folder. All items were in one folder, normally there are Applications, Setup, Media, Downloads, etc. folders, but now there are none. I can create new ones, but they are just blank gray folders, they don't have the symbols on them like the default do. I reset to default theme and it works fine, even went back to DC7 and still no folders. Uninstalled and reinstalled it, no change. Never had this happen before with a theme.
That happened to me 1 time also, not with this theme but another. Had none of the extra folders you mentioned., I had to uninstall it and reinstall it. Seemd to be a glitch on the install.