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IIRC while the folder with the user data is always lowercased, the case of the user name will be determined by the first access to the user record. If that happens to be in lowercase, the user will be in lower case from then on until the data is discarded from memory (typically a restart). IIRC the reason is the use of 'users' for both SCM users and actual accounts (and the former can become the latter), and the (Windows) disk storage incompatible names (e.g. email addresses with brackets).
Debug Jenkins and add a breakpoint in the User.get(...) functions, and you should see the first access to the user record after the start being in lowercase.