This has been an issue that has plagued me a few times. The problem is that when you are publishing from Rational Application Developer to a remote WAS instance, you get a message "Failure Uploading Archive to Server", and in the server logs, you see:
Download is not from .../config/temp/download configuration repository: /publishrecord.remote
Upload is not to .../config/temp/upload configuration repository: /
The source of the problem is that you have a leftover deployment still sitting in your temp directory. Whenever RAD publishes to WAS (don't you love IBM's acronyms), it copies the EAR file to " <wasprofileroot>/config/temp/". I found mine under:
/QIBM/UserData/WebSphere/AppServer/V6/Base/profiles/default/config/temp (this was an iSeries install....so don't freak out about the install directory).
This was on WAS 188.8.131.52 and RAD 184.108.40.206.
Once I deleted this, I was able to upload the file fine, and RAD successfully published. You might want to bookmark this as it WILL bite you in the future.