This isn't a known issue, we're going to need logs to see what is happening in the background. Here are some instructions for collecting logs, you can add these to a case.
1. Open the Protect GUI and navigate to Tools > Options > Logging and change logging to All for both user interface and services.
a. If you are unable to set logging via the GUI see this doc: http://community.shavlik.com/docs/DOC-22938
If you can reproduce the issue on demand, proceed to the next step. If not, skip to step 7.
2. Close the Protect console GUI.
3. Stop the following services
a. Shavlik Protect Console Service
b. ST Remote Scheduler Service (In 9.2, the ST Remote Scheduler Service is no longer used on the console. You do not need to stop this service if using 9.2)
4. Delete the contents of the C:\Windows\ProPatches\Logs folder.
a. Only perform this action on the Protect console server if you are troubleshooting agentless scheduling\deployment issues on the Protect console.
5. Delete the contents of the following folder (path is dependent on OS):
a. Windows Vista & later: C:\ProgramData\LANDesk\Shavlik Protect\Logs
b. Earlier OS’s: C:\Documents and Settings\All Users\Application Data\LANDesk\Shavlik Protect\Logs
6. Start the 'Shavlik Protect Console' service and open the Protect GUI.
7. Attempt to reproduce the issue, please document steps to reproduce. Screenshot are very helpful.
a. Collect the logs from the Logs folder from steps 4 and 5 (please zip)
b. Include applicable screenshots.
c. [Deployment issues only] On the target system, zip and send a copy of the entire C:\Windows\ProPatches folder and its contents (exclude the Patches sub-folder).
8. Zip everything together, reply to case email and attach to send to support.
Let me know if you have any questions.