SHow corners? Perhaps the corners of the lens hood? If that's the case you probably don't have it set properly; make sure it's firmly seated and locked in. Or, perhaps you're using a 3rd party hood?
There's some amount of vignetting (easily auto-corrected in most processing programs) when on the wide side of the 17-40, but you still get full use of the sensor.
And you are probably not using low profile filter. I can stack 2 low profiles filter on 16mm just fine.
If it's the Canon 16-35/2.8L II you're referring to, that uses 82mm filters. The 17-40 uses 77mm.
"Slim" filters tend to be more expensive. And some of them don't have threads on the front, so need a special lens cap.
B+W's "standard" mount filters are pretty slim to begin with (tho they to offer slim, as well)... I've never had any vignetting problems with them on even the widest lenses. But I also would never stack a polarizer on top of a clear "protection" filter. Previous response to remove the clear filter first, before installing the CPL, is correct.