I always tell people to never use /system/media for boot animations. This is something that was taught to me a long while back by a guy MotoCache1 on Droid forums. The reason is because the Android system looks in 2 places for animations - 1) /data/local and if it doesn't see anything there, it defaults to the /system/media where the original one is placed.
He suggested using the /data/local one for custom ones because then all you need to do to go back to "stock" is delete the ones in /data/local and you are G2G - it defaults back to /system/media. Otherwise, you have a large number of people bombarding forums asking the inevitable question: "Oh, HELP! I need the original/stock boot animation, so I can return my <insert device here>. I did a factory reset but it didn't change the boot animation."
Not sure why it stays stock for you, but I can guarantee if you put it in /data/local, it won't be an issue.