I have some suspicion I'm not explaining this very well, so i'll try again.
With themes that use the getCustomAlbumThumb function, zenphoto will indeed generate a thumbnail at the *size* it specifies. Which is great and dandy, only I can't figure out how to get this function to automatically use the crop height, width, and x y positions I've selected in my admin and which I can see are stored in the sql database. So for me this function tends to generate not crops at all but only resizes. If there is a way to get it to access these stored data, I would love to know, as that would seem to circumvent the trouble with the theme options entirely.
But the real mystery I was trying to report is that in themes where printAlbumThumbImage is used, it uses the correct crop area, and displays the thumbnail at the width and height I specified in theme options (100 x 161), but when i use "view image in a new window" it is always revealed that the actual size of the image is something... else. Since making the original post I have tried many combinations of height and width in the admin area, and have been totally baffled by the results. At first it looked like it would obey the width I asked for but always return a height of 62, but since then it's gotten much more confusing. I really cannot tell how it is picking the numbers it is picking. I have some vague suspicion it is trying to make the saved thumbnails roughly the same ratio as the original, but at this point, who knows.
This seems to leave me with a choice between an image that is a correct size but cropped on an irrelevant part of the image or is the entire image scaled down (even if the original dimensions don't match, which is also awkward looking) or with a display of the image that is a correct area, but saved at the wrong size so it has to be scaled by the browser and looks shoddy.
I tried clearing the cache but the newly generated images aren't any better.