There were source list issues fixed back in 6.0.4 so this sounds odd, but this can hang over from the previous version, or you can show/hide it using the Show Source List in the View menu - so check that first.
If using the options in the View menu doesn't help, then try this.
1) Quit RapidWeaver
2) Open the Terminal.app (found in Utilities in Applications) and enter the following command:
defaults delete com.realmacsoftware.rapidweaver6 "NSSplitView Subview Frames Main Document SplitView"
3) Re-boot your Mac
4) Launch RapidWeaver
With best regards,