Googling more on possible synctex issues led to:
- 
http://tex.stackexchange.com/questions/25578/why-is-synctex-in-tl-2011-so-fussy-about-filenames
- http://forums.fofou.org/sumatrapdf/topic?id=2131346
which seems to highlight some changes on synctex in TL 2011 (I had forgotten to 
say that I had also upgraded TL).
The file name given to synctex should now be given as a full path (which seems 
to be a new feature) and furthermore the path must end with a /./ (which seems 
to be a bug).

I'm not sure if it is the cause of my problems. I think that for forward search 
it must be taken into account inside aquamacs but for backward search skim must 
be in control, no?
>From what I understand, the backward command send the filename (%file in the 
>preference window). In which form is sent?

Fabien

Le 12 oct. 2011 à 14:01, Christiaan Hofman a écrit :

> 
> On Oct 12, 2011, at 13:49, Dagnat Fabien wrote:
> 
>> Hello,
>> I would like to know if any other aquamacs + skim user has recently lost 
>> synchronization. And I would to track down the cause.
>> 
>> Last week, I upgraded to lion and yesterday I upgraded skim. Since then, 
>> synchronization has a strange behavior.
>> 
>> On multiple file source document the synchronization from aquamacs to Skim 
>> only work when launched from the main source file (jumping rightly to the 
>> right position). When using it on an auxiliary file, skim only raise 
>> (showing previous position) and no red point appear. In that case console 
>> shows:
>> 12/10/11 10:55:41,853 Skim: SyncTeX was unable to find location and page.
>> It used to work like a charm...
>> 
>> Backward synchronization (from Skim) simply stopped to work. On console, I 
>> get:
>> 12/10/11 11:01:20,125 Skim: SyncTeX was unable to find location and page.
>> 12/10/11 11:01:24,132 Skim: kCGErrorIllegalArgument: 
>> CGSRegisterCursorWithData2: Invalid hot spot (outside of cursor bitmap)
>> 12/10/11 11:01:24,132 Skim: kCGErrorFailure: Set a breakpoint @ 
>> CGErrorBreakpoint() to catch errors as they are logged.
>> 12/10/11 11:01:24,132 Skim: kCGErrorIllegalArgument: 
>> CGSRegisterCursorWithData2: Invalid hot spot (outside of cursor bitmap)
>> ...
>> 
>> I ask myself wether it is :
>> - a lion issue
>> - a syntex issue
>> - a skim issue
>> - an aquamacs issue
>> 
>> Until now, I have tried downgrading to Skim 1.3.17 and rebooting but it does 
>> not help.
>> 
>> Any ideas anyone?
>> 
>> Fabien
> 
> We did not change synchronisation. So it must be in the information Skim 
> gets. Best chance is that's due to synctex, but I really can't say.
> 
> I don't think the messages after the first have anything to do with it, they 
> also occur a full 4 seconds later (which is a very long time in computing).
> 
> Christiaan
> 
> 
> 
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---------
Fabien Dagnat -- Maître de conférences
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 Mel : fabien.dag...@telecom-bretagne.eu
 Web : perso.telecom-bretagne.eu/fabiendagnat
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           Département Informatique
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