First, try a simple rescan of your apps. Trigger a rescan using the keyboard shortcut ⌘⇧U (COMMAND-SHIFT-U) or by quitting the app from the menu item using the gear icon and relaunching it from the dock while holding ⌘+⌥ (COMMAND-OPTION).
If MacUpdate Desktop continues to function improperly, make sure Spotlight is still able to search your Applications folder. MacUpdate Desktop relies on Spotlight to scan for apps.
If Spotlight is scanning the appropriate locations and MacUpdate Desktop is still failing, your Mac may have a corrupt Spotlight index. Have Spotlight reindex your Mac by following the directions in this Apple Knowledge Base article.
After reindexing your Mac, if MacUpdate Desktop continues to fail, it may be necessary to use Disk Utility to repair your disk.
If you have a feeling that your issue doesn’t quite fit in with these troubleshooting steps, please contact us directly and we’ll be happy to help!