If you are running Sophos Anti-Virus for Windows 2000+ in 'safe mode' (the Windows troubleshooting mode) on-access scanning is not enabled. This is because the services required by the on-access scanner are not run by Windows in safe mode. This means that while you are in safe mode, files that you open will not be automatically scanned by Sophos Anti-Virus.
You can however, run an on-demand scan in 'safe mode with command prompt' using SAV32CLI. Use the command line parameters to specify the scanning options.
Safe mode is designed to be a troubleshooting mode which only provides the minimum number of services and processes, and should only be used for troubleshooting. One of the services that the Windows safe mode does not make available is the one required to run on-access scanning.
If you think you may have a virus infection, start your computer in safe mode and then use SAV32CLI to run a scan from the command line. When you use the command line in safe mode, Windows Explorer is not started. A number of viruses can attach themselves to Windows Explorer.
For information on disinfecting your computer from safe mode with the command prompt, refer to the knowledgebase article, Removing malicious files with SAV32CLI.