I'm in Ubuntu 13.04 64 bits and I've noticed that my windows change of workspace themselves, that's very annoying and I want to fix it.
I couldn't say when it changes exactly. But I've noticed that they changes when I press Alt+Tab to change the window, suddenly, my window has changed of workspace!! It specially happen when the window to I switch with alt+tab if it was moved in the screen by me, above all if it was moved near to the edges of the screen.
It has happened from the beginning of my installation of Ubuntu and I've found anyway of fix it in compizConfig neither ubuntu tweaky tool.
I'm not sure how you're getting the windows into different workspaces in the first place, but if you want to put them back, Ctrl-Alt-Shift-Arrow will allow you to move them between workspaces.
For a more permanent solution, if you don't want to use workspaces at all, you can use the compizconfig-settings-manager to disable them. Open the settings manager, select the General Options then Desktop Size tab. Set the horizontal and vertical size to 1 and you will no longer have multiple workspaces.