The .id column that is auto-generated when calling ldply on a named list seems to be stored as character vector. It should better be created as factor with the same order as given in the input list:

l <- list(b=1, a=2)
d <- ldply(l, function(i) data.frame(x=i))
levels(factor(d$.id))

Returned: "a" "b", Expected: "b" "a".

Workaround:
levels(factor(d$.id, levels=names(l)))

I'm not sure if this is easily achievable with .parallel=T, but I wouldn't mind if the order was messed up in this special case.

(plyr 1.7.1 from CRAN)