Are the originial clips you're adding and then adjusting AVIs? Digital video? I've found Screenblast/Vegas' light and color adjustments very effective.
Just speculation but, if your older clips are MPEGs, might the flickering be caused by the video effect being applied to the key frames (re MPEG's compression method) but not the tween frames?
If your older clips are from analog video, are they saved as MJPEG AVIs?
i would suggest this---
take your older clips and process them individually in MS and save them as 4:3 avi files. take one or more and burn them to dvd (rw if your player will play them) and see if you still have the jitter.
if not, delete those files in your big avi file, and just replace them in the timeline with your new avi files. burn again to rw in 4:3. then check to see of they still have jitter...
somewhere along the process of elimination you will find the culprit....