Donna,
It appears you are talking about publishing the project,
rather than generating into the !SSL! directory.
Perhaps you have two publishing locations enabled in the
Single Source Layout setup.
Go to Single Source Layouts, select (but don't run) the
setup, select Properties and navigate through the sequence to the
WebHelp Publish dialog.
Perhaps you'll find two setups checked.
On the other hand, if you are generating but not publishing
the project, look at "Select Output Folder and Start Page" in the
first dialog of the WebHelp layout. Make sure it shows the correct
path.
Harvey