Maybe having a matte key on your V1 is causing the problem. A matte key effect needs to be over some background on a lower track to function correctly. If your background consists of a graphic over black, you might try moving everything up a layer, so the matte key keys over something.
Our company does those Vonage spots that are all over the place. If you look at one that has a white card at the end with store logos, you will see a soft-edge wipe (supplied as an animated key window) to a graphic with 4 store logos and a web site/phone number graphic. The master spot is supplied to us with the soft wipe to the end graphic already built-in, so we need to soft wipe-on the store logos and URL/phone #. The main spot is on V1 with no EFX. V2 is left empty. V3 is 5 nested matte keys created using the collapse tracks effect, and V4 is the animated key window with a matte key effect applied. If I do not leave V2 empty, the matte key does affect V1. Leaving V2 empty does leave V1 untouched.
One other thing to check is that you unselect “downstream key” on all your effects when building complex composites. That definitely will screw up the logic.
I hope some of this helps.
Bill Stephan
Senior Editor/DVD Author
USA Studios
New York City