I found the culprit and it is not Protobuf. 
Our project uses groovy, and as such I installed the Groovy Eclipse
plugin which incidently contains an Eclipse JDT patch. Removing this
patch makes everything compile normally.
I filed a bug on the groovy bug tracker.

Sorry for the noise,

On Thu, 2009-09-10 at 16:53 -0700, Kenton Varda wrote:
> Doesn't make any sense to me.  Let me know if you find a solution.
> On Mon, Sep 7, 2009 at 8:16 AM, Brice Figureau <brice
> +...@daysofwonder.com> wrote:
>         Hmm, more information on the issue below:
>         On Mon, 2009-09-07 at 16:52 +0200, Brice Figureau wrote:
>         > I'm using eclipse (3.5) on a large project using protobuf
>         v2.1.0, and
>         > I'm encountering tons of strange Eclipse java compiler error
>         on every
>         > protobuf java generated code.
>         >
>         > All the errors looks like this one:
>         >
>         > The method mergeFrom(Message) is ambiguous for the type
>         > GeneratedMessage.Builder<Bot.PBBot.Builder>
>         I created a new java eclipse project and added only the
>         generated java
>         files, and they do compile fine, so the issue is certainly the
>         compilation of the combination of those generated files and my
>         other
>         java files...
>         But I'd appreciate any help...

Brice Figureau
My Blog: http://www.masterzen.fr/

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