Since upgrading to Mountain Lion I have come across a few issues.
Firstly, if I log on, the Sophos shield is sometimes not in the menu bar. On-access scanning is still enabled (InterCheck is running and it detects EICAR test file), but it's just reassuring to see it. I did go to the menu and select "Show Status in Menu Bar", but it would not work. Curiously, it was already checked in Sophos Preferences.
Also, occasionally, I get a "fatal error" in the Console logs and it says that it is unable to configure virus detection engine. When this occurs, either the icon goes grey or totally disappears. In this case, there is no protection at all.
I did check the forums and there was a temporary "fix" where selecting "Update Now" would update the product and re-enable on-access scanning.
I assume this is because Mountain Lion is relatively new. Hopefully it will be fixed very soon.
I am on version 8.0.6C.
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