Upon shutdown of Minecraft I get a warning about failing to delete natives.
snip (normal Minecraft starting/closing no errors)
[09:51:37 INFO]: Game ended with no troubles detected (exit code 0)
[09:51:37 INFO]: Deleting C:\Users\Osky2918\AppData\Roaming\.minecraft\versions\1.6.4\1.6.4-natives-1937786569312
[09:51:37 WARN]: Couldn't delete C:\Users\Osky2918\AppData\Roaming\.minecraft\versions\1.6.4\1.6.4-natives-1937786569312 - scheduling for deletion upon exit
END
There is not that big of a deal but here is what I think is wrong.
I have my game dir outside of /.minecraft/ so something is not correct, it should be able to delete the files...
The files are in use, therefore the folder cannot be deleted, but it is deleted at the exit of the launcher: