It seems that the problem is with good old Helvetica. Acrobat Professional identifies the "boxed" fonts as:
Helvetica
Type: Type 1
Encoding: Ansi
Actual Font: Helvetica
Actual Font Type: TrueType
According to FontBook, this Helvetica is installed on my system:
PostScript name Helvetica
Full name Helvetica
Family Helvetica
Style Regular
Kind TrueType
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
Version 7.0d20e1
Location /System/Library/Fonts/Helvetica.dfont
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
Enabled Yes
Duplicate No
Copy protected No
Embeddable Yes
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!