PS:  I've committed a workaround that seems to fix the symptoms ( rev. 
47020/1 for 2.9.0 and 2.8-patched), but it would be good to fix the real 
problem.

John Chambers wrote:
> There were a bunch of red herrings in your example, but the end result 
> is at least as weird.
>
> Near as I can figure, it's a bug in the evaluator when assigning a local 
> function call object that is then modified.  I'll look a bit at the 
> code, but someone more expert in the innards of the evaluator might be 
> needed.
>
> All you need is to do one of the setGeneric() calls.  The clue is to 
> look at a utility function in the methods package that constructs a 
> function call to .Method.
>
> The bug is that after the first call, the definition of the utility 
> function has been modified to contain the results of the call.  So all 
> the arguments from successive calls accumulate!
>
> The minimal example is below.  Look at the "call <-" line the second 
> time the function .makeDotsCall is printed:  it has the arguments from 
> order() in the expression on the right hand side.
>
> At a guess, for some reason object "call" isn't marked correctly in the 
> NAMED() field, so the evaluation of, e.g., call$na.last <- 
> as.name("na.last") overwrites the expression in the definition of 
> .makeDotsCall.
>
> John
>
>  > methods:::.makeDotsCall
> function (formals)
> {
>     call <- quote(.Method(...))
>     if (length(formals) > 1) {
>         idots <- match("...", formals)
>         for (what in formals[-idots]) {
>             eval(substitute(call$NAME <- as.name(WHAT), list(NAME = 
> as.name(what),
>                 WHAT = what)))
>         }
>     }
>     call
> }
> <environment: namespace:methods>
>
>  > setGeneric("order", signature="...",
> +             function (..., na.last=TRUE, decreasing=FALSE)
> +             standardGeneric("order"))
> Creating a generic for "order" in package  ".GlobalEnv"
>     (the supplied definition differs from and overrides the implicit 
> generic in package "base": Signatures differ:  (...), (na.last, decreasing))
> [1] "order"
>
>  > methods:::.makeDotsCall
> function (formals)
> {
>     call <- quote(.Method(..., na.last = na.last, decreasing = decreasing))
>
>
> Michael Lawrence wrote:
>   
>> There seems to be a bug arising when using multiple S4 generics with "..."
>> as the signature.
>>
>> The following code works as expected:
>>
>> ##############################################################
>>
>>   
>>     
>>> setGeneric("rbind", function(..., deparse.level=1)
>>>     
>>>       
>> standardGeneric("rbind"),
>> +            signature = "...")
>> Creating a generic for "rbind" in package  ".GlobalEnv"
>>     (the supplied definition differs from and overrides the implicit generic
>> in package "base": Signatures differ:  (...), (deparse.level))
>> [1] "rbind"
>>   
>>     
>>> rbind(1)
>>>     
>>>       
>>      [,1]
>> [1,]    1
>>   
>>     
>>> rbind
>>>     
>>>       
>> standardGeneric for "rbind" defined from package ".GlobalEnv"
>>
>> function (..., deparse.level = 1)
>> standardGeneric("rbind")
>> <environment: 0x83862f4>
>> Methods may be defined for arguments: ...
>> Use  showMethods("rbind")  for currently available ones.
>>   
>>     
>>> removeGeneric("rbind")
>>>     
>>>       
>> [1] TRUE
>>   
>>     
>>> rbind
>>>     
>>>       
>> function (..., deparse.level = 1)
>> .Internal(rbind(deparse.level, ...))
>> <environment: namespace:base>
>>   
>>     
>>> setGeneric("order", signature="...",
>>>     
>>>       
>> +            function (..., na.last=TRUE, decreasing=FALSE)
>> +            standardGeneric("order"))
>> Creating a generic for "order" in package  ".GlobalEnv"
>>     (the supplied definition differs from and overrides the implicit generic
>> in package "base": Signatures differ:  (...), (na.last, decreasing))
>> [1] "order"
>>   
>>     
>>> rbind(1)
>>>     
>>>       
>>      [,1]
>> [1,]    1
>>   
>>     
>>> setGeneric("rbind", function(..., deparse.level=1)
>>>     
>>>       
>> standardGeneric("rbind"),
>> +            signature = "...")
>> Creating a generic for "rbind" in package  ".GlobalEnv"
>>     (the supplied definition differs from and overrides the implicit generic
>> in package "base": Signatures differ:  (...), (deparse.level))
>> [1] "rbind"
>>   
>>     
>>> rbind(1)
>>>     
>>>       
>>      [,1]
>> [1,]    1
>>
>> ##########################################################
>>
>> That is, rbind(1) always returns the expected result. The rbind() generic is
>> set, then removed, the order() generic is set, and the rbind() generic is
>> set again. No problems.
>>
>> But in a new session, this code breaks, where the rbind() generic is not set
>> before the order() generic:
>>
>> ########################################################
>>
>>   
>>     
>>> setGeneric("order", signature="...",
>>>     
>>>       
>> +            function (..., na.last=TRUE, decreasing=FALSE)
>> +            standardGeneric("order"))
>> Creating a generic for "order" in package  ".GlobalEnv"
>>     (the supplied definition differs from and overrides the implicit generic
>> in package "base": Signatures differ:  (...), (na.last, decreasing))
>> [1] "order"
>>   
>>     
>>> rbind(1)
>>>     
>>>       
>>      [,1]
>> [1,]    1
>>   
>>     
>>> setGeneric("rbind", function(..., deparse.level=1)
>>>     
>>>       
>> standardGeneric("rbind"),
>> +            signature = "...")
>> Creating a generic for "rbind" in package  ".GlobalEnv"
>>     (the supplied definition differs from and overrides the implicit generic
>> in package "base": Signatures differ:  (...), (deparse.level))
>> [1] "rbind"
>>   
>>     
>>> rbind(1)
>>>     
>>>       
>> Error in .Method(..., na.last = na.last, decreasing = decreasing,
>> deparse.level = deparse.level) :
>>   object "na.last" not found
>>
>> ##############################################################
>>
>> It looks like something is trying to send the parameters of order() to an
>> rbind() method. Weird..
>>
>> Thanks,
>> Michael
>>
>>   
>>     
>>> sessionInfo()
>>>     
>>>       
>> R version 2.9.0 Under development (unstable) (--)
>> i686-pc-linux-gnu
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
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>>
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>>
>>   
>>     
>
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