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As far as I can tell, the default git executable is "git", not git.exe. That works on both Windows and Linux if the PATH setting includes the directory which contains the git executable.
I assume your master node is a Windows machine with a Linux slave, and you set the Git location in the Jenkins global configuration to either be git.exe, or to be c:\Program Files\Git\bin\git.exe. If you'll set it to "git" rather than "git.exe" (or leave it unset), I believe it will work in both environments.