Sparkle updater seems to be broken or having issues
Permissions would be my last thing to check, since if they were off, the app wouldn't even run - but it's also an easy thing to rule out. Be aware that Apple's permission repair does not affect user directories (where permission errors actually tend to hurt people) or third party software (since Disk Utility only corrects permissions on software Apple installed with the OS and updates).

This seems much more likely to be an issue with the app communicating back to the server the developer of the app has set up to serve updates. I'd start with the support for the app in question and see if you can verify the update server is alive and reachable from your network.

There were some update bugs a while back, but most of them seem to be squashed in the more recent versions of sparkle that developers can download.

https://github.com/andymatuschak/Sparkle/issues?state=open