You could try running ADB as root and see if that helps. Other than that, you can just uncheck the "DATA" option in flashtool, that way you won't lose your data, thus you won't have to set everything up again. Worked for me last time I was messing around. Also, are you sure your bootanimation.zip is correct? The right folders, the settings in the text file right etc.
"However, if you put any trust in Benchmark Scores you could use them
to prove that dancing naked for 5 minutes in your garden affects device performance" - Chainfire