I appreciate it. Actually, it bugged me a little, too. The smaller ones were from a movie and when I ripped it, they came out smaller. I couldn't think of any other clips to use so I just stuck with those....
Yes, I know the problem. I encountered it many times. But you can remove the black lines of the clips in 2,40:1 (and the 16:9 ones), or add black lines to the 4:3 clips so all your clips are the same, using VirtualDubMod.
I've explained how to do that in a post at the bottom of this page:
http://www.lcficmbs.com/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000487
Actually, I had explained it to remove possible colours lines after a Rip, but it's the same way to proceed to change the ratio of a clip.