It looks like it's time to purge your caches! Go Edit>Purge>Everything that can be purged. That last part isn't what it says, but that's what it means; my machine is tied up, so I can't check what it really says.
I have no idea what you are doing in this comp or what values you are getting in the matte layer. If it's not a cache issue, and I suspect it is not, I think there is a workflow and procedure error. To diagnose the problem we need to see all the layers in the timeline with the modified properties of the layer giving you problems revealed (press the U key twice), and we need a detailed description of your workflow. You could be trying to pull the onsite in Premiere Pro and have incorrect alpha or white and black levels. The layer order could be wrong. There could be blend mode issues. Sorry, but I have no idea how to fix your problem because I have no idea how you got to this point.