Thanks for posting all of these details! Very strange but we have seen similar problems before and should be able to help.
Let’s post this over to the Admin chat to see if anyone recognizes what might be going wrong. Please feel free to join the chat, too! 
You're invited to talk on Matrix
Some other things you could post back while we are waiting for a bit more context:
- Does this only happen with specific tools? Just Minimap, or?
- Does this only happen with a particular file type? BAMs?
- Is this a new server? Or is it new behavior? Did you upgrade recently?
- What version of Galaxy are you running?
- If you run the job on a local or different cluster (if possible), what happens?
XRef → Private Galaxy Servers