I will move this over to the firecloud forum and someone from the cromwell/firecloud team will help you out with it.
When you revisit the Method Configuration tab and hit the "Launch Analysis" button, you should see whether you have checked the box for "Use Call Caching". If you have enabled this feature, the program should recognize the files which have already been analyzed and will proceed to the next step by hitting "Launch Analysis."
Call caching should be turned on by default. More information can be found here