Clearing the cache under preferences just deletes the temporary files that Captivate creates as you edit project files. It has nothing to do with your Preferences.
If you want to reset your preferences back to defaults you need to delete the Captivate Preferences folder in your OS user profile. The location of this folder varies by OS.
I only have access to WinXP at the moment so the path on my current machine for this folder is:
C:\Documents and Settings\myuserprofilename\Local Settings\Application Data\Adobe\Captivate 5.5
In Win Vista/7 it will be in a slightly different location (perhaps someone else can chime in with that today).
Just close down Captivate, delete or rename this folder, then restart Captivate. It will re-initialise your Preferences (including any custom Workspaces you set up) so that they are now reset to what they were when Captivate was first installed.