Performing a virus check

There's actually no advantage to doing this as MSE scans downloads as they're saved to disk just as quickly.

See: How to add MSE's scanner to Free Download Manager

Did you use the Path and  Arguments with proper syntax as in the refernced thread?

C:\Program Files\Microsoft Security Client\MpCmdRun.exe

-scan -scantype 3 -file %file%

I use Free Download Manager (v.3.9.3.1600) myself and can confirm MSE will scan and logs as an event (well two actually ID 1000 and ID 1001) and also to MpCmdRun.log.

Event Type: Information
Event Source: Microsoft Antimalware
Event Category: None
Event ID: 1000
Date:  10/26/2013
Time:  10:37:35 PM
User:  N/A
Computer: Q-58744232957F4
Description:
Microsoft Antimalware scan has started.
  Scan ID: {D7B6AD35-0EB5-4DA2-A4D0-D99BF57BC133}
  Scan Type: Antimalware
  Scan Parameters: Custom Scan
  Scan Resources: file:_C:\Documents and Settings\Administrator\My Documents\Downloads\sbsetup.exe
  User: Q-58744232957F4\Administrator

For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.

Event Type: Information
Event Source: Microsoft Antimalware
Event Category: None
Event ID: 1001
Date:  10/26/2013
Time:  10:37:47 PM
User:  N/A
Computer: Q-58744232957F4
Description:
Microsoft Antimalware scan has finished.
  Scan ID: {D7B6AD35-0EB5-4DA2-A4D0-D99BF57BC133}
  Scan Type: Antimalware
  Scan Parameters: Custom Scan
  User: Q-58744232957F4\Administrator
  Scan Time: 0:00:12

For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.

MpCmdRun.log
C:\Documents and Settings\Administrator\Local Settings\Temp

MpCmdRun: Command Line: "C:\Program Files\Microsoft Security Client\MpCmdRun.exe" -Scan -ScanType 3 -File "C:\Documents and Settings\Administrator\My Documents\Downloads\sbsetup.exe"
Start Time: ‎Sat ‎Oct ‎26 ‎2013 22:37:35

Start: MpScan(MP_FEATURE_SUPPORTED, dwOptions=3, path C:\Documents and Settings\Administrator\My Documents\Downloads\sbsetup.exe, DisableRemediation = 0)
INFO: ScheduleJob is not set. Skipping signature update.
Scanning path as file: C:\Documents and Settings\Administrator\My Documents\Downloads\sbsetup.exe.
MpScan() started
Time Info - ‎Sat ‎Oct ‎26 ‎2013 22:37:47 MpScan() was completed
Finish: MpScanStart(MP_FEATURE_SUPPORTED, dwOptions=16385)
Finish: MpScan(MP_FEATURE_SUPPORTED, dwOptions=16385, path C:\Documents and Settings\Administrator\My Documents\Downloads\sbsetup.exe, DisableRemediation = 0)
Scanning C:\Documents and Settings\Administrator\My Documents\Downloads\sbsetup.exe found no threats.
MpScan() has detected 0 threats.
MpCmdRun: End Time: ‎Sat ‎Oct ‎26 ‎2013 22:37:47

With the proper arguments, you can call either a Quick Scan or a Full Scan with the user interface (msseces.exe), but not a Custom Scan (scan of a single file, folder, or drive). So you need to use the command line utility (MpCmdRun.exe) to scan a file or folder. Since the command line syntax for a Custom Scan is:

-Scan -ScanType 3 -File

…the arguments provided here would presumably be correct:

http://www.freedownloadmanager.org/board/viewtopic.php?f=1&t=14151&hilit=security+essentials+virus+scan

GreginMich