Fonts in pdf files show as squares

My new lion imac renders some fonts in pdf files as squares. I trensferred applications and setting from my old snow leopard macbook which was working ok. Problem appears in preview, skim, filemaker but not in adobe reader. Seems like the lion pdf renderer is not working correctly?

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!

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