I'm guessing that you must be using the Free Transform tool, which has limitations like these where it doesn't necessarily know the way you spin the tool, just the final amount. So since the Free Transform tool gives you -90 degrees, it tweens that way. I'll file it though, to see if there's something we can do. You can be sure to get the outcome/direction you expect by using percentages in the Transform panel (you can drag the hot text to spin it, which is kinda useful), or using the Motion Editor, to make sure it goes the correct direction.
I was not actually using the free transform tool, I was using the menu option Modify>Transform>rotate 90 CW. Does that just generate the same change as using the free transform tool?
I see what you mean about the transform panel. I have never really looked at that before.
Ah yes, the menu option - indeed it seems to behave the same, yes. I'll make sure that's added to the bug I filed, thanks for noting it.