After upgrading to Lion interface alignment seems to break, any ideas?
First, do a Safe Boot. This, among other things, clears the Mac OS X font caches. There are also several third-party GUI tools for clearing the font caches, and there is a command-line command for doing this in the Terminal; can somebody else please provide the details?

Second, this may be a long shot, but have you used TinkerTool or a similar utility to change system font default point sizes? If so, try setting everything back to its default.

TinkerTool has many other wonderful capabilities, but its font point size settings are not practical simply because Mac OS X has never reacted well to changes in the font point size in the user interface.

Have a look at the screen shot below. It shows the TinkerTool interface set to the proper default system settings for all fonts. You can use this to confirm that everything is set to the correct default.