You can try the GCG (and possibly some of the other herbs) from sensiblehealth.com - I use that before flushing and it does crush a lot of stones. I recommend going to that site and you can email them(I forgot their names) about your problem. They usually get back to you quickly and are very helpful.
I had a problem with my 1st flush also, and that helped after a while. And as someone said, a lot of people do recommend doing another flush again or at least another dose of ES - you'd be able to try that quicker than waiting for the herbs to come in the mail, if you think it is getting serious.
FYI - I took me a while to do my 2nd flush, but I just did this past weekend and it was soo much better. Seems to me that is fairly common.