@atreidex
For reference, instructions for 'Upgrading Showkase' can be found here.
The process of upgrading Showkase replaces the core Showkase files and leaves all your existing pages untouched.
There should not be any problems in upgrading a Showkase site but it would be wise to make a complete backup of your existing site first, just in case anything goes wrong and you need to reinstate your original files at a later date.
I didn't get to do a system repair (not sure how I'd do that either)...
Go to 'System -> Repairs' from within the Showkase interface.
... but simply waiting 15 minutes it changed back over to my normal live pages...
It sounds like there may have been some kind of issue with your web server (such as server-side caching) but hopefully everything's OK now.
If you continue to experience difficulties, then please let me know and I'll try to help you out.