Another good question. For now changing the rotation period doesn't actually do anything except for visually change how fast the Earth (or any planet) is spinning. The climate sim is always assuming the Earth rotates on its axis once every day (86,400 seconds). The one exception to that is if you've tried the 'Tidally Lock' button, you've seen what happens when the rotation period is equal to a year. We check only for that one special case of slow rotation, and not all possible rotation rates.
So for the purposes of the 90 degree obliquity you were trying, even though you set rotation period to zero, it was still acting like the rotation period is 1 day, so it makes sense that the "top" and "bottom" of the planet don't get cold like the usual poles do, like you might have been expecting to happen. The poles remain the poles and completely melt when they are facing the Sun, and freeze again when they're not.
This is surprisingly difficult to fix given the way that we do the calculations, but it's on the long-term list.