If so, is that agent configured to only run on the BIX node? (assuming this is the Pega Cloud)
If the agent is running on a non-bix node, the output will be generated on the wrong node.
If that doesn't appear to be the issue, we'd probably want to have a closer look at the logs and maybe enable some debug. An SR would be appropriate for investigating further. (If you open one, be sure to update this post with it)
If you're running the extract manually, the extract will produce output on the Web node you are on (as opposed to the BIX or UTIL node where it should be running). It's possible that could be related to the issue, so keep that in mind when investigating. You may want to enter an SR for this as well, as troubleshooting these types of issues can be difficult. If you enter an SR, please update this post with the SR number for tracking purposes.