My mistake - and just to clarify. The system in question is MS2003 (NOT 2000). The server is FMS8.
Like I said, it's at another location and I was working from memory.
Have you rebuilt & optimised the problematic database? (Filemaker advanced has these tools). Is this a database that you have upgraded from a old version (before v7) of filemaker, if you have then there is most likely a layout with corrupted data on it. Is it possible to rewrite/rebuild it by importing the fields & scripts to a new database & recreating the layout/s from scratch. & why not merge the three database togeather?
There should be no problems with having FMS & FTP running on the same machine. & I would not advice having FMS & SQL running separately on the same machine, the server would not optimise very well, they are both memory & Hard-drive intensive processes...