Hi psk_rh an welcome to the RH community.
Do you mean that when you click on a topic in the TOC that
the topic opens in ne window? If so, I seem to remember that is do
to the window being used in the single source layout. I think it is
specifically caused where the default window was created when the
default single source layout was other than Microsoft HTML Help.
Try deleting the current window and adding another one whilst
Microsoft HTML Help is your default single source layout. Then
ensure this window is selected in the properties of your single
source layout.