Internal Error when trying to deploy

We're having trouble trying to deploy our livecycle application. We have a version that works and deploys, but if we many any change (no matter how trivial) the application will not deploy, and we will be given an "Internal Error".
I read this:
http://blogs.adobe.com/livecycle/2010/05/internal_error_when_checking_i.html
but our problem isn't with checking in files, our problem is with deploying them.
In any case, we synchronized the clocks through windows. We're working on setting up a local time server for all of our machines to sync to just in case this is causing the problem, but I don't think it is.
Any advice on how to get around this Internal Error, what it means, or what causes it, would be appreciated.
Thank you.

Hello Javan,
We were actually able to fix it. We had some dependencies left over from files that we deleted and were no longer using. After we removed the dependencies manually from the .process_dependency file, everything worked fine.
Thanks.

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