I have just made a new build of my game using 5.1.1p3 since it doesn't work with 5.1.1f1, and when I test the built game the mouse input is acting weird. This is what I use to fetch the input in an Update function: if (Input.GetKeyDown(KeyCode.Mouse0) || Input.GetKeyDown(KeyCode.Space)) and if I use the Space button all works fine, and if I use the mouse button it has delays (which are not fixed or constant). Was running on firefox, and no I don't have a bad hardware. I was waiting so long for this new patch to come so I can publish an update of my game, but seems like I'll have to wait for another week.
I notice the same thing: Framerates are all fine, but clicking on buttons are much slower, sometimes they never register until I click off and then on the frame again. I think this is a new issue to 5.1
I got an answer from the Unity QA that this issue has been fixed now and will be available in the next release.
I'm using Unity 5.1.2p1 and it appears to be fixed in this patch. You can download it from here: http://unity3d.com/unity/qa/patch-releases