I'm running SEP 11.0.4202. Over the weekend SEP started flagging a critical program file in our payroll system as a trojan horse, and I believe this is a false positive. (I've submitted the file to Symantec). In order to be able to use our software, we need the file.
On the server in question, I disabled Auto Protect, then went into Centralized Exceptions and added the file in question. For what it's worth, the file is AFWREG.FLL. Now, my understanding is that SEP should ignore that file and not scan it anymore, but it quarantined it again. I went through the process again, and this time it seems to be left alone, for now at least.