Did you place the box above the floor in the model? You don't have to be very precise just make sure it above the floor in the model and so it covers the area where the light poke through?

For your Superfly settings, I would suggest the following changes, not that i think it will solve anything, but just as general settings:

Pixel samples: 8 (Will be ok for quick preview renders)

Progressive refinement: Turn that on (Not sure why you would ever render without it on, maybe someone with better knowledge of Superfly can explain why? :))

Max Bounces: 4 (You need that to render glass correctly from what i can see)

You might or might not be able to increase render speeds by enable or disable "Seperate process" in the settings under render. But you will have to test out what works best for you.

Leave the rest of the options to whatever you want, seem to have no impact on render speed or quality from what i can see, tried to put 512 in them which made absolutely no different. If you want to increase quality just increase pixel sample (23 should give you rather good quality).

Always use render region when testing, no need to render the whole image, just mark the area that you are interested in, will be a lot faster.

But then again im not an expert in Superfly so someone will most likely correct me and maybe it have something to do with materials or something, the information about Superfly is really lacking unfortunately. So these settings are just what i found to be working well. :)