I am new to all this Jailbreaking, so please bear with me.
I have an Iphone 3Gs OS4.1, which I have successfully JB'd and have Cydia, Winterboard etc installed.
I have installed a theme but it did not change the FolderIconBG or the FolderSwitcherBG.
I used iPhone Browser and found the default images for these two items and saved them to my PC. I opened them up in PS to edit and then saved them.
Then I dragged them into iPhone Browser to overwrite the existing ones.
On checking my iPhone, I found that the FolderIconBG had changed to my edited version but that the FolderSwitcherBG was still showing the default Linen style.
After searching the net, I found many different topics about this and people saying to delete:-