Yeah I have had that problem. The thing is other applications don't ALL (some do!) suffer this repeating jerk when compensating NTSC>PAL so I don't think it is impossible for them to get rid of it.
Are you using the latest version? 0.4.x.x
I'm sure mine seems smoother since that version. I'm going to try the file which was really jerky in the previous version - I'll post back this eve!