*I'm using some naruto episode*
Unless you have them from a DVD and followed the guide... There shouldn´t be a problem.
You are using a compressed material and that causes always problem:
-Problem with framerates
-DAMN slow for editing (if you want to edit directly in Premiere)
-Quality
...
(that´s for all sort of compressed codecs like: mpeg, wmv, x264, xvid, divx...)
There are only reasons against it.
-Load into VDM
-Clean up footage with avs (stands in link; tutorials) with DirectShowSource
-export clips in looseless stuff
-use looseless stuff in Premiere
-Export your project out of Premiere looseless
-Load it into VDM or zarxGui for x264
-Compress it
-Announce it
Stands everything in this guide:
http://www.animemusicvideos.org/guides/avtech/
oh well and don´t use Naruto =/ I'm getting more than sick of it and buy your footage in future. Thanks