WEU was awful tool to be used and could corrupt map easily.
As for the anti-virus, I can explain it to you.
JNGP and WEU inject his own code into the process of WE. Most tools allow to setup an exception for such cases, some have to be turned off though (like Kaspersky)
Avira Antivir detects several of the files as trojans, you can choose ignore for the reports and whitelist those files later to fix the problem. (Extras\Configuration, activate export mode, under both Scanner\Scan\Exceptions and Guard\Scan\Exceptions add the offending files to the list)