It would appear that this maybe by design - Upgrade keep the same folder structure while NEW installs receive a new folder structure:
Agent 4.8.0 - Page 29: On Windows Vista, Windows 2008 Server and Windows 7 64‑bit client systems, the default location is: :\program files (x86)\mcafee \common framework
Agent 5.0.0 - Page 31: If not specified, the default location is: :\program files\mcafee\Agent
Yeah, I've seen references in McAfee documentation (can't remember which offhand) that state that upgrades from 4.8 or before will have the old structure, and new 5.0+ installs will have the new. Makes it fun when you've RDP'ed to a box and want to get the shield icon up; do you go to the old location or the new one to run cmdagent.exe /s?
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