Howdy,
I ran into the same issue some time ago and I found an easy workaround.
On my machine, most of the time the problem happens when I minimize the file application list, then I maximize the application and I return to a non maximized window. When I try to reopen the file application list, I got the error message.
After closing the application, I comment (actually I delete them) the three lines from the TopoFusion.ini file, as shown below (those starting with ActiveList), save the file and the problem is (at least temporarily) fixed.
The TopoFusion.ini file can be found, on Windows XP, in the following location:
C:\Documents and Settings\<username>\Local Settings\Application Data\TopoFusion"
[Position]
Height=12168
Width=19908
Maximized=0
;ActiveListMinimized=0
;ActiveListLeftMinimized=0
;ActiveListTop=155
Hope it will help,
Stefano