It appears that the problem has resurfaced. It looks like the local storage or cookies are overriding what the bookmark says to do.
I went to my bookmark, and it was correct. Then I changed the settings to enable 3D mode and zoomed out. The next time I used the bookmark, it showed me that same thing, instead of the zoom of the bookmark.
Also, when in 3D mode, the zoom level of the URL doesn't always change when the view changes. It sometimes does zoom level 3 and 4 twice.

Hey! Today the zoom level did not change! That's much better.

I love windyty, and use it to see the weather forming by looking at the pressure overlay. So I set it up how I want to see it (pressure and zoom) and then bookmark that page. The next time I return using the bookmark, the URL does not match the zoom level. I prefer to see the big picture and so zoom to level 4, but windyty changes it to zoom level 5 and it is reflected in the URL.