There is no known issues with JaCoCo on Windows.
The only thing which was done recently - is to make sure that JaCoCo can be built on Windows (something with zero changes from end-user perspective) and JaCoCo own tests and integration tests pass on Windows, which is the case as of today.
So probably problem lies somewhere around your usage/configuration. More details about your environment and setup are required to give more precise answer.
Best regards,
Evgeny