Yes, the preferences showing up altered and/or blank as shown in the screen shots is fully repeatable upon initial launch of PM. In the 2nd set of screen shots I did not reset or OK any of the preferences. If I just close the window and open it again, everything appears back to normal. Once the preferences are back to normal they don't change again until I quit PM and launch it again.
I've been playing around some more and just figured out why the altered preferences actually took effect on those few occasions (like the blue background and the missing cache folder). When I first started trying out 4.6 I was playing with preferences lots, so I must have hit the OK button after changing a preference, for example, in the General window, not realizing that the preferences had altered themselves in the Preview, Cache and Color Management windows.
So now all of this is repeatable: when I launch PM and open preferences, they appear altered/blank. If I just close the window and reopen it, my correct preferences return and remain until I quit and launch again. On the other hand, if I OK the window, the altered/blank preferences stick and I get the blue preview background, missing cache folder etc again. At this point I will have to manually change all the preferences back to the way I prefer and click OK.
If I do OK the altered/blank preferences, there is one more peculiarity: even though all the check boxes appear blank, the actual preference may still be in effect, or not. I haven't tested them all, but for example the "Show soft rotation indicator" preference continues to work, whereas "Auto-center thumbnails in thumbnail gallery" does not, even though all the boxes in the Preview window are unchecked.