I think sometimes these problems may be caused by incorrect namespace or category settings. If you uninstall and reinstall an extra, it can create a new namespace and/or category, but not overwrite existing objects that didn't get uninstalled. Those objects now have a namespace or category that no longer exists.
Custom Property Sets are particularly susceptible to this. MODX won't remove them unless they were created by the extra, but their category ID may no longer exist. They may show on the properties tab of the object, but not in Tools->Property Sets and they may be ignored when you try to use them.
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PLEASE, PLEASE specify the version of MODX you are using.
MODX info for everyone:
http://bobsguides.com/modx.html