I'm not familiar enough about any differences between ESX 4 and ESX 4 (Service Console).
Can you turn on Verbose Shell Logging and re-try scanning the system. This will give much more detail of why it's failing in the daily log file.
1. Run Regedit
2. Navigate to:
[HKEY_LOCAL_MACHINE]\SOFTWARE\Foundstone\Foundscan\Tweaks] (for 32-bit host) or
[HKEY_LOCAL_MACHINE]\SOFTWARE\Wow6432Node\Foundstone\Foundscan\Tweaks] (for 64-bit host)
** if the key "Tweaks" doesn't exist, create it. **
3. Add the following Value:
LogShell DWORD Value 'ff'
4. Rescan, and look in the ~Foundstone\Logs\LogFile.<date>.txt for any errors associated with the userID you specified in the scan.
If it's not obvious, open a Service Request, and attach the daily log.
I hope that helps!