I believe this is fixed as discussed in email (but put here to make it public).
 There was a call to substitute() in the R code to get the name of the eSet, but
I had put an as() call before that in case an exprSet was being passed in.  In
that case the substitute would return a blank name, so you likely were running
into having multiple datasets named "".  I submitted a fix, see if that helps
things.