When you change the game directory, the launcher ignores the new directory and uses the normal C:/Users/Username/appdata/Roaming/.minecraft.
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This has happened to me a couple of times, but sometimes it loads the correct directory. I think it's a 50-50 ratio of occurrence.
I'm running the 1.3.3 launcher currently.
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Something just occurred to me. This only happens with the directory folder that I also named ".minecraft" and no other directories. I will try renaming this folder and see if the issue turns up again. It may be possible naming your directory folder after the one in the appdata confuses the launcher.
Confirming that this happens to me as well. I'm on a Mac though, and the Launcher recognizes the saves from the new directory, but the ignores the Versions folder. A bit different, but main problem happening to me as well.