After upgrading after Lion (circa 3 months ago) more and more interfaces seems to just break. It's easiest if see it yourselves!
Anyone know how to fix this issue?
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.
I have seen this many times before. It's a safe bug, i.e. it won't affect your data, only the look of fonts on screen. The problem in this case is the font Helvetica (and any of it's variations). Apple uses a TrueType version of the font, and you probably somehow replaced it with a PostScript or OpenType version.
Each font has a baseline where all characters' "bottoms" align to and letters with descenders like 'g, j and y' will let their lower parts hang from. Even if the font is named the same, the baseline set by the creator of the font can be different from TrueType to OpenType and so on... Therefore this bugs happens.
Simply find out why your Helvetica has been modified and change it back, if possible. Eeither you or someone replaced the font in the /System/Library/Fonts/ folder, or you are using a font manager (Suitcase, FontExplorer Pro, etc.) that can change fonts in the system.
Whatever you do, you need Helvetica (and quite a few variations of it, as well as others) always be present in your system, they need to be available before any font manager is loaded. Otherwise your system will become unstable. The OS doesn't care what kind it is, as long as it is present.
You can have a look at this excellent document by Extensis, downloadable here:
It covers the fonts that are mandatory, which ones can be removed, and lots lots more.