It seems that the problem is with good old Helvetica. Acrobat Professional identifies the "boxed" fonts as:
Type: Type 1
Actual Font: Helvetica
Actual Font Type: TrueType
According to FontBook, this Helvetica is installed on my system:
PostScript name Helvetica
Full name Helvetica
Language Afrikaans, Albanian, Azerbaijani, Basque, Belarusian, Bulgarian, Catalan, Cornish, Croatian, Czech, Danish, Dutch, English, Esperanto, Estonian, Faroese, Finnish, French, Galician, German, Greek, Hawaiian, Hungarian, Icelandic, Indonesian, Irish, Italian, Kalaallisut, Kazakh, Latvian, Lithuanian, Macedonian, Malay, Maltese, Manx, Norwegian Bokmål, Norwegian Nynorsk, Oromo, Polish, Portuguese, Romanian, Russian, Serbian, Slovak, Slovenian, Somali, Spanish, Swahili, Swedish, Swiss German, Turkish, Ukrainian, Uzbek, Vietnamese, Welsh, Zulu
Unique name Helvetica; 7.0d20e1; 2011-04-05
Copyright © 1990-2006 Apple Computer Inc. © 1981 Linotype AG © 1990-91 Type Solutions Inc.
Trademark Helvetica is a registered trademark of Linotype AG
Copy protected No
Glyph count 2.194
I guess there is a Helvetica mix-up. The PDF seems to contain a Type 1 version, which is substituted with the standard Apple system Helvetica dfont version, but they don't match.
This is indeed a long-standing problem, not really Lion specific. But I would have thought that by now it would have been solved. Why all those conflicting font formats and encodings anyway? What a mess this is!
Do they look like this?
If so, those are generated by the font LastResort. That can be caused by a missing font, or cache files corrupted badly enough that they can't be read.
Close all running applications. From an administrator account, open the Terminal app and enter the following command. You can also copy/paste it from here into the Terminal window:
sudo atsutil databases -remove
Terminal will then ask for you to enter your admin password. As you type, it will not show anything, so be sure to enter it correctly.
This removes all font cache files. Both for the system and the current user font cache files. After running the command, close Terminal and immediately restart your Mac.
Although the original poster never replied, I'm going to chime in.
This is a common problem, look here: http://apple.stackexchange.com/questions/24209/this-pdf-displays-with-question-m arks-instead-of-letters
The simplest solution is to use Adobe Reader for Mac, although other approaches are listed here and there.