I had the same problem. There is a bootanimation.zip in your data/local folder. Run terminal emulator and type in:
su
mountsys
rm /data/local/bootanimation.zip
unmountsys
sync
The phone looks in both folders at boot but takes data 1st
yes thanks I found that out a while ago, I just manually copied and pasted the animation I wanted to use into the data/local folder using root explorer instead.