I'm the user with the problem. I get it on every Ren'Py game I've tried.
Note: it only happens if you
start the game in fullscreen mode. If you start windowed and then toggle full-screen it's fine (until you quit and launch in fullscreen mode). I've had this happen in every Ren'Py game I have, across all publishers, but non-Ren'Py games don't have this particular issue.
My computer is a 2014 15" MacBook Pro Retina on 10.9.5. I doubt it's Mavericks because I have a 2010 15" MBP non-Retina running 10.9.5 and it doesn't have this problem.
I've narrowed it down to something with the embedded intel graphics card. If I disable automatic graphics switching to force it to run on my NVIDIA 750M, it'll run perfectly fine (though drain my battery a lot quicker). Resolution seems to have something to do with it too. I run in a scaled 3360x2100 (native is 2880x1800, but even that doesn't look right, in a different way). If I crank it up to 3840x2400, I see a much smaller piece of the bottom left-hand corner and all the buttons are really big (but still unclickable) - on Intel, all resolutions are OK on NVIDIA.
I don't know if this helps, but here's the spec for the Intel card:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel (0x8086)
Device ID: 0x0d26
Revision ID: 0x0008
gMux Version: 4.0.8 [3.2.8]
And the fully-functional NVIDIA GeForce GT 750M:
Chipset Model: NVIDIA GeForce GT 750M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 2048 MB
Vendor: NVIDIA (0x10de)
Device ID: 0x0fe9
Revision ID: 0x00a2
ROM Revision: 3776
gMux Version: 4.0.8 [3.2.8]
Unfortunately, only the 15" model comes with the NVIDIA card option. Everyone with a 13" rMBP is stuck using the Intel card.