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I'll ask someone from my team to look into your report. I'm not sure why there would be a difference.
As a test, have tried with the /prods switch? If you know you want Endpoint Encryption specifically, try
\\myserver\mer.exe /prods "Endpoint Encryption" /save \\myserver\MER.tgz /silent
Info on command line switches can be found at https://kc.mcafee.com/corporate/index?page=content&id=KB59385
Question: Do you have ePO in your environment? Have you looked into use ePO-MER instead?
thanks just tried the ePO-MER. Checked-in the package and extension, tried to run the task to deploy MER on 2 machines and it failed with this error :
2013-01-18 16:03:59 E #4980 ScrptExe Failed to copy C:\ProgramData\McAfee\Common Framework\Current\SUPPCLNT1000\ServicePack\0409\Mer.exe to C:\Program Files (x86)\McAfee\Supportability\MER for ePO\Mer.exe. Setting bRet to FALSE
The result is that only 2 dlls gets installed and not the actual mer.exe. If I install this manually with the .msi it works...
Anyway, now I've set the policy to gather as much information as possible (8) and ran the scan task from ePO with the option to gather logs for all detected softwares.
The result is the same thing, I still get a fraction of logs that I usually get from running MER manually on a machine... (23mb vs 1.6mb)