So may times a long bout of troubleshooting with a pesky problem ends up being something obvious. It is not always obvious when virus protection is causing a problem. When I reach that first point of scratching my head saying "this doesn't make sense" I try to make a point of eliminating antivirus from the mix and testing again.
Often the software vendor will have recommendations on which of their working directories or configuration files need excluded.
Check out this great resource for Microsoft Antivirus Exclusions