If you had saved your profile tools in or under the "My Profile Tools" directory on the 5.2 version, it would have copied them over to the new data path location.
On XP:
c:\Documents and Settings\All Users\(Shared)Documents\Thermwood\eCabinet Systems
On Vista/Windows7:
c:\users\Public\(Public) Documents\Thermwood\eCabinet Systems
If you had them saved some place else, they will still be at that location.
It sounds like you are still viewing the files from the old 5.2 location. We do not remove anything you have created, but the directories that the 5.2 install put there will be removed (hence the non-existent Whiteside, CMT USA, MDF Asymmetrical Tools and Amana Tool dirs ). Make sure you go to your tools via the new user data path (see my last post for the XP -- Vista/Win7 differences). Drop down the "Look in:" combo box on the tool selection dialog to verify that the path is completely the new one.
OK, I found them in My Documents. I remember poking around on the beta version and finding stuff there. Really surprised that the public version still puts things there instead of in a Thermwood specific area.