The advantage of Geosetter is that you can put all of your tracks into one folder, select just the images you want to geotag and then point the program to the folder containing your tracks - no need to select individual tracks. Even images taken over a period of months will be tagged as long as the corresponding track is in the folder.
Yes, that is the one. I use it to tag Olympus raw files, it does recognise Canon .cr2 and .crw files. Geotagging is the first thing that I do before editing any raw file, even changing the name.
Sounds like you are on to something, but, a couple of questions:
1. Which version of Windows.
2. When you say "modified date" in Windows Explorer are you referring to what one sees in the general files view or are you looking in the Properties:Detailed view after selecting a specific picture file?
3. How are you transferring the files from the camera or camera card to your Windows machine? If you are using a program which one?