Can you post a screen-cap of your Timeline zoomed-in?
From the description, it sounds like you are experiencing "shearing" of Frames. I have encountered this, when I moved a Clip too hard against another Clip, with Snap ON. When I have done that, a Frame, or two, have been sheared off, and can appear before the next Clip, or, depending on exactly what one is doing, they might end up out at the end of the Timeline, beyond the Tail of the last Clip. Without seeing what you are encountering, we can only guess.
>AVI clips that were created in ArcGIS
Also, what is the actual codec inside the AVI file... and what is ArcGIS?
Read Bill Hunt on a file type as WRAPPER http://forums.adobe.com/thread/440037
What is a CODEC... a Primer http://forums.adobe.com/thread/546811
What CODEC is INSIDE that file? http://forums.adobe.com/thread/440037
Report back with the codec details of your file, use the programs below... a screen shot works well to SHOW people what you are doing
ArcGIS is a mapping/geographic analysis software and one of it's features allows you to export movies of geographic events that have a time element (I am using it to show the movement of tagged fish during the spring). I had limited options for the Codecs I could use with that program and found that the Microsoft Video 1 (listed in the properties screenshot below as CRAM) was one of the only ones that actually worked.
I also just noticed that if I previewed the clips in the clip monitor, even before I put them in the timeline, I was getting the same problems with the first frame being wrong (either a blank screen or a random frame from elsewhere in the clip). For instance, in the clips below Figure 3 is what the first frame should look like, but instead I am getting the black screen in Figure 2. Is this some sort of importing issue? I also noticed in the properties that is says the clip has "dropped frames". Is that an issue?
Figure 1. Properties
Figure 2. First frame of the clip - blank screen
Figure 3. The second frame of the clip - what should be the actuall first frame
I have not really studied your issue nor followed this thread. I was visiting here for other reasons when your thread caught my attention. I was just browsing through your screenshots and their details and wondered, "Do you really have and want video clips with a frame rate of 1 frame per second?