We've seen this a couple of times with different versions of FME 64bit and ArcGIS 10.2.1 with 64bit background processing installed. It typically involves ArcGIS 10.2 and Geodatabase that is on Oracle.
The problem isn't related to FME. It is due to missing patches for ArcGIS. To prove the problem is with ArcGIS only, you can isolate this to ArcGIS libraries by using arcpy and background processing to interact with the Geodatabase SDE (Oracle). This will present the problem with a hanging process.
The solution is to install the "Utility Patch series 6" software for the ArcGIS 10.2.1.
- ArcGIS-1021-BGDT-OCPU-Patch (64bit Background Geoprocessing Oracle)
- ArcGIS-1021-DT-OCPU-Patch (Desktop Oracle)
- ArcGIS-1021-DT-UTU1-PatchB (Desktop Telecomm).
Once these are installed the ArcGIS 64bit background processing and the FME workspace will function correctly.