No, the preview bounds don't seem to have any effect on the pallette.
Here are the results I get when I distribute evenly. The clipped PDF image has the black box grouped to it.
If I add the black box inside the clipping mask, the distributing is based on the bounds of the clipping mask
I think it is the right behavior so I cannot help you. Actually now that I look at it I am not sure I understand what you are saying and seeing.
in any case I don't think I can help you.
The align pallette acts differently based on whether or not a clipped object has something grouped to it.
Clip an image, and then align the clipped image with another object. It works fine.
Clip an image, and group another element to the clipped object. The align pallete now changes it's behavior. (it aligns based on the original bounds of the image, and not the clipped bounds.)
That's a much clearer explanation. ;-) I see the same behavior, and I would call that a bug.
I wonder if it's related to the lame way that symbols distribute as well. Maybe behind the scenes, they're considered a group too, though that doesn't explain why they align wrong as well.
I'd report it and hope they get it in CS5, since they don't seem to want to fix any bugs like these for free anymore.
We have a 50-50 chance that Adobe will care to fix anything.
The ridiculous icon preview bug was introduced in CS3 version and proudly shipped with CS4.
I promised to buy CS4 after the release of its update. What you know, I saved money this year!
I will wait to see what bugs CS5 will have, and hope Adobe will actually care to "fix" for CS6.