It's been a while since I did this myself, and I have not installed SH3 recently after getting a new pc. So I'm a bit rusty on the details.
As said, SH3Gen only works if you made a savegame. It needs to load that to get the intelligence. I think I kept the gane running in the background myself, but it may not be appropriate. I've seen suggestions to close the game. Maybe because SH3Gen cannot change the files is SH3 has them still opened in memory. It's only concerned with those savegame files, and as such the savegame must be reloaded in the game for the map markers of SH3Gen to become apparent.
As for Taktukgis, iirc it (maybe SH3Gen too) installs by default into the Program Files folder somewhere. And I noticed it, or SH3Gen tries to save the generated GIS maps in a subfolder there. (maybe fixed in later versions) Since Vista the OS doesn't like that and aborts it, so it is better installed elsewhere, not in Program Files. (I think you know that drill already.) Maybe that is preventing the files from being generated.
Does the following thread match what you are experiencing?
http://www.subsim.com/radioroom/show...ghlight=sh3gen
..., if so then file associations for .ttkgs files may not be set correctly. It can be changed with default programs in the configuration panel:
http://pcsupport.about.com/od/fixthe...-windows-7.htm