You can go to Sites > Advanced > Recreate site cache to have the site cache be reset by DW.
DW does have a cache file as well that might have some part to play in this, here are some instructions for clearing this file:
common_installation_issues.pdf
You should also try setting up a new DW site without the FTP and try to make use of Security Assist first, then go back and update the FTP info to ensure that none of the info or settings are being affected by Security Assist.