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
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
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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: