So you did a test run and it appeared to work, then you did a regular run and all your beads went to waste again....is that correct?
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I think this goes back to what "snetmcom" said, if there are beads in the waste then they must have passed through the filter at some stage. They shouldn't be able to do this so it must be the source of your problem.
There are several washes of your beads on the filter, during one wash an aliqout is taken off to the QC output (before enrichment). This should happen even if your emPCR has failed. If you're not getting anything in the QC output then it looks like your beads are passing through the filter for some reason. Probably a good idea to check your lot numbers with your rep.
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