Steps to reproduce this issue:

1. Open the attached project
2. Open 'ScaleOnMouseEnter' scene
3. It has 2 cubes and 2 other 'blocking' cubes in front of them
-Right blocking cube with TransparentFX
-Left blocking cube with IgnoreRaycast
4. Play the scene
5. Hover the mouse over left blocker cube
6. Even though layer is 'IgnoreRaycast', the cube behind it does not receive OnMouseEnter()
7. Hover the mouse over right blocker cube
8. Even though the layer is 'TransparentFX',raycast is ignored by blocker cube and received by the cube behind it

Results in 4.6 are exactly the opposite

Captured reproduction of the bug: http://screencast.com/t/inrRbcRXdpFt (right-5.0, left-4.6)