This kind of problem can happen when a dataset has not fully loaded. Or it may have been truncated upstream (before loaded to Galaxy), or while performing other data manipulations in Galaxy. Or, the assigned datatype is incorrect. However, given that the same data is readable when you modify workflow settings (or inputs?) indicates that is not your issue.
Mixing compressed/uncompressed inputs, submitted together in a batch (collection or multiple individual datasets), might be the problem. If you are submitting the data in a dataset collection, all collection datasets need to have the same datatype assignment.
Check to make sure all datasets grouped together for the same tool “input” are either compressed or uncompressed, assigned a datatype that matches the actual data format/content, and are all the same.
This is just a “best guess” about what is going wrong. So please check, adjust data if needed, then write back if you need more help. An issue with the workflow settings, or some upstream tool, would be the next troubleshooting step.
FAQs for datatypes/metadata: