sharan,
that's the reason why it is called bootANIMATION and not bootVIDEO ;-)
"the bootanimation is not a video, as such. it is rather couple of png files displayed after each other. so dont expect 25fps ;-)"
"also note that the default shiny "android" animation is done in a VERY different way, directly coded into the bootup sequence!"
in parallel to the animation you see visually, a lot of things are going on inside android. i guess, if you have a fast cpu and SDcard, images will be displayed faster. why it's faster, if images are in 1 folder, i don't know. i may guess that zip extraction from 1 dir is faster then from more dirs.
you may also want to try to use png instead of jpg. _depending on your animation_ the png files _may be_ simpler/smaller (loaded decoded/faster).