I am facing the same issue even after updating June CU, Restarting the Box, Provisioning a new Search Service Application and restarting the search services.
using “Get-SPEnterpriseSearchMetadataCrawledProperty” returns only the Out of the Box “Default” properties, and all the custom crawled porpoerties properties are not listed, although all the custom crawled properties are listed in the Search Schema UI page in Search Administration, Anyone could help or point what I may be missing.