I am not sure.
PDF is a native format in OS X. So it looks like all applications can create a PDF using OS X. Leading one to believe that all applications would act the same way. Which was the case using Pages and TextEdit.
So it looks like it is a OS X issue.
My OS X 10.6 has the problem but OS X 10.7 works correctly when creating a PDF.
If it is a MacOs x problem you could first try a safe restart. Restart your computer. Press the Shift key when you hear the starting chime. Keep it pressed untill you see a bar emergin on the screen. Let it work, might take some time. Log in and try Preview and Pages again. Then restart again the normal way.
If it works all is fine otherwise you can install MacOs 10.6 again ontop of what yo have. You don't have to do a "clean" install. Dont forget to do the system updates. I usually have first downloaded the Combo updates for the system before I do a system inallation.
Yes it means it can't find the character.
Since you are using both Japanese and Latin input it could mean the two are crossed over somewhere. pdf files usually only contain subsets of font characters, especially when they are huge sets like Japanese fonts.
Hard to tell exactly what is going wrong without being able to get at the file and fonts.