Having the same issue
Although this issue is about a year old I am getting the same thing I think.
Site is working and I thought to add CMS (Design Extender 1.06)
Connection works just fine in Dreamweaver I think (screen shot). However, when trying to connect through WebAssist I get a MYSQL Error #2013. Times out and I close the file.
I have deleted the entire site and reinstalled, deleted the database and re-connected .. not sure what would be next to try.
Any help would be appreciated.