JInput: Event.getNanos() doesn't match System.nanoTime()

I’m creating an application in which I need to know if an event has happened before a certain time. Thefore I wanted to compare the events nanos with a nanotime I stored earlier with System.nanoTime().
The problem is that the value returned by System.nanoTime() is bigger than the nanos of all events that happen in about the first 10 seconds after calling System.nanoTime() (on Windows).
I also tried running the same program on Linux but than the difference was even bigger.

Does the JInput event system use a different time than the systems nanotime?

Thank you in advance!