If system-wide environment variables have been set via /etc/environment those are not accessible if they exist in lower-case and capital case letters. Jenkins combines both variables into a single one, and updates the first detected variable with the value of the second one. Here some examples:
Jenkins should not modify set environment variables because it will cause problems with tools which rely on the right capitalization. One example is mercurial which needs the lower case version of the proxy configuration. It will no longer work when both variables are set.