Possible Bug In "Clean-Up" Tool
Hmm.. I noticed that when the GSA Clean-Up tool is executed, all GSA does is go through the site list and then adds the working sites to identified. What this dose is causes duplicates... and if you are using GSA mainly for blog comments, that means that you will constantly keep getting the "already parsed" error every time you run this tool since GSA dose not post the same comment to the same URL twice.
Shouldn't GSA search through the sites list, delete the non working, and simply leave the working ones alone? Or did you purposely design it to do both? (meaning, it dose as mentioned above with the exception of it adding the working url's to "identified" as well.)