I know that JTC files are SDE connection files with the extension changed from 'sde' to 'jtc'. They are not stored in the folder with the normal sde connection files. Where do they get stored?
These are usually stored in: %ALLUSERSPROFILE%\Application Data\ESRI\WMX\Database
XP: C:\Documents and Settings\All Users\Application Data\ESRI\WMX\Database Win7: C:\ProgramData\ESRI\WMX\Database
However that location can be modified by the WMXAdvancedSettings.exe, located in %ProgramFiles%\WMX\Bin (C:\Program Files\WMX\Bin\WMXAdvancedSettings.exe). This application changed the ConnPath value under HKEY_LOCAL_MACHINE\SOFTWARE\ESRI\JTX