the ~new line signifies the end of the popup and so anything following that won't be shown because as far as litestep is concerned the popup has ended.

!new signals the start of the popup and ~new signals the end.

likewise a line similar to this:
*Popup "litestep" Folder
indicates the begining of a folder.
all subsequent entries will be placed in that folder and the end of items intended to be placed in that folder is signified by ~folder.

my explanation seems really poor but i hope you get the gist