In fact, the update process continues even if you tap outside of the progress bar dialog and dismiss it. But in any case, this is indeed an unwelcome scenario.
This is a known defect that was fixed in a subsequent iFix release for the 5.0.6.2, 6.0.0.2 and 6.1.0.1 fix packs releases.
- If you are an IBM customer or business partner, you can get the latest ifix for your version/edition from Fixcentral.
- Otherwise, you can download the latest Developer Edition (non-customer) of the 6.1.0.1 ifix from Eclipse Marketplace. Or download a zip file of the latest 5.0.6.2 or 6.0.0.2.