Normally we add a post workflow action and click wait until completion and give it a large number of time to wait.
We had a workflow action that we didn't check off must Success required, it just didn't wait for completion. 4.9.81 (yes, I know its old, but this behavior is out of the ordinary, usually It does wait for completion.)
Inside the workflow a batch file that runs a java program creates files and than returns and inside of the workflow we copy the files into the Jobs\Job_currentjob folder. We noticed that if we looked into the folder on the server the files were there, but the zip didn't contain them until we did what was below which is clicking off the Success Required box. The other parameters were the same
Release : 4.9
Component : CA Test Data Manager - Javelin
Open a support case and ask for the latest TDM 4.9.1 Portal patch.