Using Multiple Masks with Effects

I’m having some difficulty with using an effect in conjunction with multiple masks , I’m hoping someone can help!
I have a shot which shows the exterior of a house and I want to show the light flashing on and off inside one of the rooms which will be seen through a window. I’m in a composite shot and I have duplicated the layer so I have two identical shots, and have re-named one of them to avoid confusion. The window itself has many panes so I have created an individual mask for each pane in one of the layers so the light effect will only be seen on the window and won’t affect the whole shot. To test that I had set up the shot correctly, I increased the brightness on the masked layer and lo and behold, just the window panes got brighter, which is what I wanted.
However, I thought it would be better to use a light ray instead so that it would provide a more realistic effect ‘through’ the window, but for some reason it will only work on one of the masks, not all of them. I have tried adjusting each of the mask’s settings but the best I can get is that the ‘last’ mask which I adjust is the only one on which the effect works, i.e. if I then adjust the next one to the same parameters then the effect disappears on the former but appears on the latter.
I’m very confused about this as the brightness worked through all the panes at once – does anyone have any suggestions as to what the issue is?
Thank you.