When managing fonts in OS X, conflicts or faults in font files can result in a number of odd problems such as misaligned characters, garbled characters, and improper fonts being used when documents are displayed, converted, or printed. In addition, font problems can result in applications or even the system crashing or hanging.
These problems can happen if there are conflicts from old font files, duplicates of the same font file in different locations in the OS, or even missing fonts that ought to be installed and active in the system.
Generally font problems are not too common since most applications people use rely on the fonts that ship with OS X (which are usually present in the system); however, there are some programs like Office and Adobe CS that can install quite a few fonts of their own. Additionally, graphic designers may install custom font libraries that can result in hundreds if not thousands of extra fonts being present on the system, and thereby increase the prevalence of odd problems and conflicts that can occur, especially if the fonts were obtained and compiled from a variety of different sources over years of work.
If issues with fonts occur, generally the first approach is to use Font Book to verify your fonts are installed in working order, followed by removing or disabling any with errors. Alternatively you can try disabling font sets in groups to see if you can isolate the problem that way. These routines can be done using Font Book, or by using some third-party programs such as FontExplorer, Font Agent Pro, and Suitcase Fusion.
Even when using these tools, font problems may sometimes be difficult to root out, and it may help to tackle the problem by disabling all third-party fonts and start your troubleshooting with only the fonts that were shipped with OS X enabled. To help with this, Apple has a list of the fonts that it includes with OS X Lion, which you can use as a reference.
If you cannot root out your font problems by any other means, then set up your system to only have the fonts on the list installed. If you do not have a preferred font manager tool installed, then you can do this by going to the following locations on your hard drive and removing all font files except those that are on the list (move them to the Desktop or another safe location):
Fonts may also be in the /System/Library/Fonts folder, but be cautious when changing fonts in this directory; some are required for proper system use, and most third-party programs will install fonts to either of the above two directories instead of to the Font directory in the system folder.
Once you have removed the fonts, you have a couple of approaches you can take. First you can try launching your programs and running them with only the basic OS X fonts present, which should, hopefully, result in the problem disappearing. After this you can then use Font Book or your font manager tool to reinstall the removed font files.
Alternatively, you can immediately reinstall the font files but then use Font Book to disable them, followed by enabling them systematically to test them. This approach may be faster, and reinstalling them all at once will ensure that the fonts are managed properly by one managing program, which might increase the likelihood that the system is using them properly.
At this point, rooting out the source of your specific problem would be a matter of systematically enabling or disabling the fonts to see if and when the problem goes away.