You developed a .NET application and signed it with a strong name, using one of the methods described in How to: Sign an Assembly with a Strong Name.
After deploying the application in your environment, you find it is detected as WS.Reputation.1.
Creating a strong-named .NET assembly is done for the purposes of versioning and naming protection. It allows the assembly to be installed in the Global Assembly Cache (GAC), located in C:\Windows\assembly\GAC. The GAC stores assemblies specifically designated to be shared by several applications on a system. Signing with a Strong Named Key (SNK) is done to uniquely identify an application, for the purpose of inter-assembly trust. As pointed out in Strong-Named Assemblies, it should not be relied upon for security. As such, it does not weigh into Symantec's software trust verification process.
Unsigned internal applications are particularly prone to WS.Reputation.1 detection, as we combine file age, file download source, digital signature, and file prevalence using a proprietary algorithm to determine their safety reputation.
In addition to strong-naming your assemblies, consider code signing them, even if the concerned application is internal only. Code signing an application will give it a good rating at the outset, thereby making a WS.Reputation.1 detection of that application unlikely (albeit not entirely impossible). Code signing can be fully automated, by adding it as a post-build event in Visual Studio.
For a Symantec-centric solution to Code Signing, see Symantec white paper To Increase Downloads, Instill Trust First.
Should you choose to forego code signing, it is recommended to submit every new version of your application via the Symantec Security Response False-Positive web site and wait until you receive actual confirmation that it has been whitelisted prior to deploying it in your environment. If you are a BCS customer, you are welcome to join our Enterprise Customer Software Whitelisting Program to greatly facilitate the whitelisting process. To do so, fill out the form at https://submit.symantec.com/whitelist/bcs/. Our Whitelisting team will then reach out to you and provide all relevant information. Note that only the Whitelisting can provide this information to you. It is not available to Symantec Support.