Roslyn Analyzers not working after converting to new csproj

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We recently converted a .NET 451 solution to the new csproj structure. In doing so our custom Rosyln analzyers (referenced as a nuget package from a private feed) seem to have stopped working, both in VS and when building manually. There are no build errors coming from that package. The new csproj is too large to post here but all the obvious analyzers stuff is in there including the package reference to the analyzers themselves and the correct CodeAnalysis properties:

<RunCodeAnalysis>true</RunCodeAnalysis>
<CodeAnalysisRuleSet>..\Standard.ruleset</CodeAnalysisRuleSet>

There is no GlobalSuppression file in the solution.

Separately for testing I have created a simple net451 class library, converted to the new csproj and seen that the above works fine. But our project is massive - the csproj alone is ~3K lines. So something somewhere is nullifying or suppressing our rules. I have pored over the entire csproj file and there is nothing obviously wrong.

Has anyone had this issue in converting a net framework solution to the new csproj structure?

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