There is a window which is eating up the nifty mouse events before they can get to my input manager. Is there any way I can set this certain element to ignore those events?
From the manual
DISABLE EVENT PROCESSING FOR INDIVIDUAL ELEMENTS The new methods to ignore mouse events and keyboard events at the global Nifty level have now been added at the element level as well. You can now ignore mouse and keyboard events for individual elements too. You simple use the same method names setIgnoreMouseEvents(true) and setIgnoreKeyboardEvents(true) for a single Element and this element will no longer process any elements. Please note that this is a bit redundant to the existing visibleToMouseEvents attributes but we've kept the same names to be consistent with the method on the main Nifty instance. The visibleToMouseEvents attribute should be used to generally define visibility to mouse events and ignoreMouseEvents / ignoreKeyboardEvents to temporarily disable access to the element.
try to call in the window element setIgnoreMouseEvents 
I hope it works!