Unfortunately, that is a limitation of the Track Matte.
One workaround would be to create a Project, just for the material that you will be animating, and do the Keyframing there - nothing else on the Timeline. Then, Export/Share that Timeline, to be Imported and then limited with the Track Matte Keying in the main Project.
You might want to create a "guide" to see the "window," that will be provided by the Track Matte, when doing the initial animation. For more info, see this ARTICLE.
The choice of that Export/Share format will depend on what you are working with. I like using one of the Lossless CODEC's (which handles either SD, or HD material), like Lagarith Lossless, or UT Lossless. There is more info in this ARTICLE. For SD material, DV-AVI is a good choice too. While it is lossey, the compression is only about 5%, and for just one generation, will never be noticed.
This limitation in Pr is pretty significant. I don't really understand the logic behind it. The technology to make a matte layer parametrically independent from the layer it is matting exists, even in other Adobe products, like After Effects and Photoshop.
Anyway, after a day and a half of frustration I believe that I have found a reasonable workaround. This workaround makes it possible to view the changes made to the scale and position of the video layer being matted in relation to the video layer behind it, without having those changes effect the the matte layer being used to mask it. (Not like with using nested tracks)
The secrete is to not use the standard Motion adjustments to change the size and position of the layer being matted. I discovered two filters in the Video Effects/Distort folder, standard Pr Effects. Effect "Magnify" changes the size of the image, and the effect "Offset" changes its position. The Track Matte Key, (or other Matte effect I'll assume) needs to be at the bottom of the list in the Effect Controls panel. I haven't tested weather the "Magnify" effect is any different (in terms of quality) than the standard "Scale" parameter which is in the always present "Motion" effect... My first impression is that there is no difference.
I hope that this saves someone some time and frustration.
What is your Pr?
Are you using any version of Premiere Elements for the work that you are reporting on? I have yet to find video effects such as Magnify or Offset in Premiere Elements (any version).
This additional information would save readers of this thread a lot of time looking for these effects in Premiere Elements.
sorry about that, I just replied to the first entry that dealt with the problem I was having, I didn't realize that it was the Premiere Elements forum. I'm using Premiere Pro CS6 and now CC. I guess this won't work in elements.