The SLiMMaker website (and download once the new release is put up) now has an "iterate" function that will produce both a motif and a set of sequences, all of which match that motif. Basically, the input sequences matching the motif produced by SLiMMaker keep getting put back through SLiMMaker using the same settings until the motif produced matches all of the input (or there is no motif produced). Obviously, if the first SLiM produced matches all of the input, this mode will behave just like the original.
At some point, I will add some more documentation, including some examples.
