Open up the Custom Property Editor and make sure your yes/no properties all have a value set. Once that's done, try reopening the UnDP.If that doesn't clear up the issue, I'd open a support ticket.
I had been having a similar issue, so I deleted the Custom Property in the editor (which was formatted as "Help_Desk") and replaced it with a Yes/No Property called "HelpDesk" (no underscore). I then went to Manage Nodes on the website, selected a node, and clicked on Edit Properties. The new custom property was indeed in the drop down menu, and I was able to select it and change True to False.
Perhaps the issue was the formatting of the first custom property?
I opened a ticket up and this worked for me:
1. Open your Custom Property editor
2. Right Click any blank space on the menu bar, you will get a Toolbar/Customize pop-up
3. Select 'Customize' & go to the 'Commands' tab
4. For categories select 'Properties' & under 'Commands' Highlight 'Update Report Schemas'
5. Drag & drop the 'Update report schemas' to the Menu bar
6. Click the new icon that appears, you should get a message 'Custom Properties have been added to all Report schemas'
Now refresh you website & see if the custom properties show up. If they still don't please run a repair on orion, apply SP2 & re-run the configuration wizard.